Re: [Freesurfer] Recon-all -all for many MRI sequences?

[Douglas N. Greve]

you have to pass it the file(s) you want to analyze. If you have a bunch 
of dicoms, and your T1 is just one of many, you have to figure out one 
of the files that corresponds to the T1. Or you can use dcmunpack, eg,

dcmunpack -src /path/to/your/dicoms -targ outputfolder -auto-runseq mgz
That command will find all the series and convert each one to an mgz 
file. Hopefully, it will be obvious after that which one is the T1


On 8/22/2024 10:48 PM, 김유진 wrote:


External Email - Use Caution

Hello,


I have many dicom files with many MRI sequences from one person.

(T1, T2, FLAIR, DWI, ...)

I didn't divided the folders according to the sequences-they are 
all in one folder.


Then does the program sort T1 image automatically and make results 
when I do 'recon-all -all -i  -s '?


Or does the program use all the files?

And I wonder that Freesurfer offers code for sorting the files based 
on sequences.



Thank you in advance!


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Re: [Freesurfer] recon-all terminates at fix topology rh step

[fsbuild]

External Email - Use Caution

 You’re using the 7.2.0 release from 2021 whereas the latest release is 
7.4.1 from 2023.   Unless you have to stick with the older release because 
floating point math results could differ with a newer one, then you could try 
downloading and installing the 7.4.1 release from the links under “7.4.1 
Release” at the top of the page,

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsOr try just running the 
subject that fails with the 7.4.1 release to see if it makes a difference.
- R.

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Re: [Freesurfer] Recon-all manual edits - multiple re-runs

[Douglas N. Greve]

It will take all edits you have made into account when you rerun it.

On 6/25/2024 1:00 PM, Blujus, Jenna wrote:


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Hi all,

I have processed a set of T1w data through recon-all (v7.3.2) and am 
now making manual edits, if necessary. I have had a few cases where 
control points, wm.mgz, and brainmask edits are needed and 
incorporated via 'recon-all -autorecon2-cp -autorecon3 -s ${id}'. 
However, upon inspection of the updated outputs following the initial 
manual edits, further edits are required only to the wm.mgz to fix new 
topological errors.


To incorporate the second round of wm edits, would I need to rerun 
recon-all from the control point stage to incorporate */_all_/* edits 
(i.e., first round [control points, wm, brainmask]) or just from the 
wm stage with recon-all -autorecon2-wm -autorecon3 -s ${sid}? 
Essentially, I am asking if each time recon-all is re-run does it 
progressively build off of previous edits?


Let me know if you need any clarification.

Thanks in advance,
Jenna

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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

And also don't expect the cortical surface to be very good once you get ont

On 6/24/2024 8:08 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> we had checked the template and compared it to the standard template 
> (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we 
> don't see anything unusual (please see screenshot). The only difference is 
> our head is smaller (probably because it's children data).
>
> Therefore, I have two questions:
> 1. Do you think that the head size could be the reason for the reconstruction 
> failure? I don't think it should be, because the reconstruction of individual 
> data has been going very well.
> 2. After creating our template, we also used the commands below to fill holes 
> and normalize. The data type of output file is float, but we find that the 
> standard template has a data type of short. Do you think the data type might 
> influence the reconstruction? In fact, we also tried to change the datatype 
> to 'short', but there were obvious problems with the output image.
>
> # Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul 
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats 
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range 
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
> Best regards,
> Chen
>
>
> - Original Message -----
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Monday, 3 June, 2024 18:42:14
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> Why did you do an lr reversal if it looked good? And when you say it
>> looks good, what do you mean. One thing to double check is that the
>> orientation looks ok. Load it in freeview. Up at the top you will see
>> little brain images in coronal, sagital, and axial. When you click on
>> one of those, the brain in the main image should become coronal, sag, or
>> axial. If this does not happen, then something is wrong.
>>
>> On 5/29/2024 10:47 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> thanks so much for you reply. Yes, I checked the template and it looks 
>>> good. The
>>> orientation was in LAS originally then I did the Left-Right Reversal by 
>>> using
>>> the command "mri_convert --in_orientation RIA". Before or after the 
>>> reversal, I
>>> got the same error message. Here I attached the template, could you please 
>>> have
>>> a look in case of any clue? Thank you so much!
>>>
>>> Best,
>>> Chen
>>>
>>>
>>>
>>> - Original Message -
>>>> From: "Douglas N. Greve" 
>>>> To: "freesurfer" 
>>>> Sent: Wednesday, 29 May, 2024 15:26:25
>>>> Subject: Re: [Freesurfer] Recon-all for a common template
>>>> sounds like something is wrong with the image. Did you look at
>>>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>>>> head?
>>>>
>>>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>>>External Email - Use Caution
>>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I tried to run the reconstruction with the command line:  recon-all -i
>>>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>>>
>>>>> then I got the error message:
>>>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>>>> talairach_avi log file is transforms/talairach_avi.log...
>>>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>>>> GNU/Linux
>>>>>
>>>>> And this is the error message in the talairach_avi.log:
>>>>> imgrege: no voxels in register
>>>>> ERROR: 'imgreg_4dfp
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>>>> status=254
>>>>> ERROR: mpr2mni305 execution aborted
>>>>>
>>>>> Does anyone know how to solve this problem? Thanks so much!
>>>>>
>>>>> Best,
>>&

Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

Sorry, I have no idea what is going wrong. Try using a full head in 
stead of skull  stripped image

On 6/24/2024 8:08 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> we had checked the template and compared it to the standard template 
> (MNI152_T1_1mm_brain.nii.gz). Our template looks normal on orientation and we 
> don't see anything unusual (please see screenshot). The only difference is 
> our head is smaller (probably because it's children data).
>
> Therefore, I have two questions:
> 1. Do you think that the head size could be the reason for the reconstruction 
> failure? I don't think it should be, because the reconstruction of individual 
> data has been going very well.
> 2. After creating our template, we also used the commands below to fill holes 
> and normalize. The data type of output file is float, but we find that the 
> standard template has a data type of short. Do you think the data type might 
> influence the reconstruction? In fact, we also tried to change the datatype 
> to 'short', but there were obvious problems with the output image.
>
> # Fill holes and normalize
> fslmaths ANTS_43Kids_template_rigid2MNI.nii.gz -bin -fillh -mul 
> ANTS_43Kids_template_rigid2MNI.nii.gz -div $(fslstats 
> ANTS_43Kids_template_rigid2MNI.nii.gz -P 100) -range 
> ANTS_QS_template_MNIS.nii.gz -odt float
>
> Thank you so much!
>
> Best regards,
> Chen
>
>
> - Original Message -----
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Monday, 3 June, 2024 18:42:14
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> Why did you do an lr reversal if it looked good? And when you say it
>> looks good, what do you mean. One thing to double check is that the
>> orientation looks ok. Load it in freeview. Up at the top you will see
>> little brain images in coronal, sagital, and axial. When you click on
>> one of those, the brain in the main image should become coronal, sag, or
>> axial. If this does not happen, then something is wrong.
>>
>> On 5/29/2024 10:47 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>> thanks so much for you reply. Yes, I checked the template and it looks 
>>> good. The
>>> orientation was in LAS originally then I did the Left-Right Reversal by 
>>> using
>>> the command "mri_convert --in_orientation RIA". Before or after the 
>>> reversal, I
>>> got the same error message. Here I attached the template, could you please 
>>> have
>>> a look in case of any clue? Thank you so much!
>>>
>>> Best,
>>> Chen
>>>
>>>
>>>
>>> - Original Message -
>>>> From: "Douglas N. Greve" 
>>>> To: "freesurfer" 
>>>> Sent: Wednesday, 29 May, 2024 15:26:25
>>>> Subject: Re: [Freesurfer] Recon-all for a common template
>>>> sounds like something is wrong with the image. Did you look at
>>>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>>>> head?
>>>>
>>>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>>>External Email - Use Caution
>>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I tried to run the reconstruction with the command line:  recon-all -i
>>>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>>>
>>>>> then I got the error message:
>>>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>>>> talairach_avi log file is transforms/talairach_avi.log...
>>>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>>>> GNU/Linux
>>>>>
>>>>> And this is the error message in the talairach_avi.log:
>>>>> imgrege: no voxels in register
>>>>> ERROR: 'imgreg_4dfp
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>>>> status=254
>>>>> ERROR: mpr2mni305 execution aborted
>>>>>
>>>>> Does anyone know how to solve this problem? Thanks so much!
>>>>>
>>>>

Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

[Iglesias Gonzalez, Juan E.]

Dear Barbara,
you could in principle use recon-all-clinical for the enhanced T1 but the 
surface reconstruction would probably fail.
Instead, I’d probably run SynthSR to synthesize 1mm T1 intensities while 
inpainting abnormalities and then run the standard recon-all.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Barbara Bellenberg 

Date: Thursday, June 13, 2024 at 3:30 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] recon-all clinical : usage with contrast-enhanced 
T1-weighted images?
External Email - Use Caution

Dear all,

I would like to use the recon-all-clinical pipeline with Gadolinium
contrast-enhanced 3D-T1 weighted images. Can you tell me if
recon-all-clinical is suitable for this purpose?

Thanks in adcance for your support!

Barbara


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Re: [Freesurfer] recon-all clinical : usage with contrast-enhanced T1-weighted images?

[Gopinath, Karthik]

Hi Barbara,

Yes, you can use recon-all-clinical for the enhanced T1. But, the surface 
reconstruction might fail and in that case, you might have to try running 
SynthSR + recon-all.

Thank you,
Karthik

On Jun 13, 2024, at 1:30 AM, Barbara Bellenberg 
 wrote:

   External Email - Use Caution

Dear all,

I would like to use the recon-all-clinical pipeline with Gadolinium
contrast-enhanced 3D-T1 weighted images. Can you tell me if
recon-all-clinical is suitable for this purpose?

Thanks in adcance for your support!

Barbara


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 .
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Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

Why did you do an lr reversal if it looked good? And when you say it 
looks good, what do you mean. One thing to double check is that the 
orientation looks ok. Load it in freeview. Up at the top you will see 
little brain images in coronal, sagital, and axial. When you click on 
one of those, the brain in the main image should become coronal, sag, or 
axial. If this does not happen, then something is wrong.

On 5/29/2024 10:47 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> thanks so much for you reply. Yes, I checked the template and it looks good. 
> The orientation was in LAS originally then I did the Left-Right Reversal by 
> using the command "mri_convert --in_orientation RIA". Before or after the 
> reversal, I got the same error message. Here I attached the template, could 
> you please have a look in case of any clue? Thank you so much!
>
> Best,
> Chen
>
>   
>
> - Original Message -
>> From: "Douglas N. Greve" 
>> To: "freesurfer" 
>> Sent: Wednesday, 29 May, 2024 15:26:25
>> Subject: Re: [Freesurfer] Recon-all for a common template
>> sounds like something is wrong with the image. Did you look at
>> ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a
>> head?
>>
>> On 5/28/2024 6:07 AM, Chen Yang wrote:
>>>   External Email - Use Caution
>>>
>>> Hi everyone,
>>>
>>> I tried to run the reconstruction with the command line:  recon-all -i
>>> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>>>
>>> then I got the error message:
>>> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>>> talairach_avi log file is transforms/talairach_avi.log...
>>> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
>>> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64
>>> GNU/Linux
>>>
>>> And this is the error message in the talairach_avi.log:
>>> imgrege: no voxels in register
>>> ERROR: 'imgreg_4dfp
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>>> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>>> talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed!
>>> status=254
>>> ERROR: mpr2mni305 execution aborted
>>>
>>> Does anyone know how to solve this problem? Thanks so much!
>>>
>>> Best,
>>> Chen
>>> - Original Message -
>>>> From: "Chen Yang" 
>>>> To: "freesurfer" 
>>>> Sent: Monday, 20 May, 2024 13:59:13
>>>> Subject: [Freesurfer] Recon-all for a common template
>>>> External Email - Use Caution
>>>>
>>>> Dear Freesurfer Developers,
>>>>
>>>> my data is from 50 preschoolers and I created my own group template from 
>>>> these
>>>> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti 
>>>> file
>>>> (see attached). Then we'd like to process this group template in 
>>>> Freesurfer to
>>>> reconstruct the cortical surfaces as the individual brain images. My 
>>>> question
>>>> is, how can i do the recon-all with the template? Because I only have this
>>>> template file I feel I don't have enough input files(?).
>>>>
>>>> Thanks in advance!
>>>>
>>>> Best regards,
>>>> Chen
>>>>
>>>> --
>>>> Chen Yang
>>>>
>>>> PhD Student
>>>> Independent Research Group 'Milestones of Early Childhood Development'
>>>> Max Planck Institute for Human Cognitive and Brain Sciences
>>>>
>>>> Email:ya...@cbs.mpg.de
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://secure-web.cisco.com/152_yjWgWiW7QaUCNWdHFdgPDgbGmCDd24wrNL32r-4bja7mb7PwZLrVrT8x_Ot8oLBlBDSrPO5K5UwFJww_c_Y6HNu9vVaziQgviXOWppVzFqlFYr7Go-t0P0ERBoTxsiCjkgkjp8sqNY12lF_6KIfy959AukP9K4eVWkLGWIlqP1lI_TQg2slA5qX1X8cEK857YHHC7vYcLM4qF7sKEU0nJ9xOLxq89J8jkqjRr9_G8fkxbUlriLEANx5HQWi_HJrmVUug78slky8NFQA8NxGyoQIVMsNUzUALsTUJfZAHI6rBpxPQLUejRDnI1ZFbAJwtYq_-f7tFE_dpFheFywA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>>> The informatio

Re: [Freesurfer] Recon-all for a common template

[Douglas N. Greve]

sounds like something is wrong with the image. Did you look at 
ANTS_QS_... ? Is it oriented correctly? Does it look like a brain in a 
head?

On 5/28/2024 6:07 AM, Chen Yang wrote:
>  External Email - Use Caution
>
> Hi everyone,
>
> I tried to run the reconstruction with the command line:  recon-all -i 
> ANTS_QS_template_MNI.nii.gz -subject CGBT -all
>
> then I got the error message:
> talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
> talairach_avi log file is transforms/talairach_avi.log...
> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
> Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 
> GNU/Linux
>
> And this is the error message in the talairach_avi.log:
> imgrege: no voxels in register
> ERROR: 'imgreg_4dfp 
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
>  
> /software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
>  talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! 
> status=254
> ERROR: mpr2mni305 execution aborted
>
> Does anyone know how to solve this problem? Thanks so much!
>
> Best,
> Chen
> - Original Message -
>> From: "Chen Yang" 
>> To: "freesurfer" 
>> Sent: Monday, 20 May, 2024 13:59:13
>> Subject: [Freesurfer] Recon-all for a common template
>
>> External Email - Use Caution
>>
>> Dear Freesurfer Developers,
>>
>> my data is from 50 preschoolers and I created my own group template from 
>> these
>> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file
>> (see attached). Then we'd like to process this group template in Freesurfer 
>> to
>> reconstruct the cortical surfaces as the individual brain images. My question
>> is, how can i do the recon-all with the template? Because I only have this
>> template file I feel I don't have enough input files(?).
>>
>> Thanks in advance!
>>
>> Best regards,
>> Chen
>>
>> --
>> Chen Yang
>>
>> PhD Student
>> Independent Research Group 'Milestones of Early Childhood Development'
>> Max Planck Institute for Human Cognitive and Brain Sciences
>>
>> Email:ya...@cbs.mpg.de
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Recon-all for a common template

[Chen Yang]

External Email - Use Caution

Hi everyone,

I tried to run the reconstruction with the command line:  recon-all -i 
ANTS_QS_template_MNI.nii.gz -subject CGBT -all

then I got the error message: 
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
talairach_avi log file is transforms/talairach_avi.log...
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Linux ramones 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 
GNU/Linux

And this is the error message in the talairach_avi.log:
imgrege: no voxels in register
ERROR: 'imgreg_4dfp 
/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2C_as_mni_average_305
 
/software/freesurfer/6.0.0p1/debian-bullseye-amd64/average/711-2B_as_mni_average_305_mask
 talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! 
status=254
ERROR: mpr2mni305 execution aborted

Does anyone know how to solve this problem? Thanks so much!

Best,
Chen
- Original Message -
> From: "Chen Yang" 
> To: "freesurfer" 
> Sent: Monday, 20 May, 2024 13:59:13
> Subject: [Freesurfer] Recon-all for a common template


> External Email - Use Caution
> 
> Dear Freesurfer Developers,
> 
> my data is from 50 preschoolers and I created my own group template from these
> kids using the 'buildtemplateparallel' scripts from ANTs. I got a nifti file
> (see attached). Then we'd like to process this group template in Freesurfer to
> reconstruct the cortical surfaces as the individual brain images. My question
> is, how can i do the recon-all with the template? Because I only have this
> template file I feel I don't have enough input files(?).
> 
> Thanks in advance!
> 
> Best regards,
> Chen
> 
> --
> Chen Yang
> 
> PhD Student
> Independent Research Group 'Milestones of Early Childhood Development'
> Max Planck Institute for Human Cognitive and Brain Sciences
> 
> Email:ya...@cbs.mpg.de
> 
> ___
> Freesurfer mailing list
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> The information in this e-mail is intended only for the person to whom it is
> addressed.  If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Mass General Brigham
> Compliance HelpLine at 
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> 
>  .
> Please note that this e-mail is not secure (encrypted).  If you do not wish to
> continue communication over unencrypted e-mail, please notify the sender of
> this message immediately.  Continuing to send or respond to e-mail after
> receiving this message means you understand and accept this risk and wish to
> continue to communicate over unencrypted e-mail.

___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

It should just run the fill step. However, I've been slowly 
reprogramming recon-all to just see what needs to be run and rerun it, 
so you might get more than just the fill.


On 5/3/2024 4:38 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will 
just run the -fill step, do I submit it on the files that have already 
been run? In addition, does this error count as Freesurfer running out 
of RAM or it's more of a cluster issue I have to talk with the staff 
that manage it?


Sincerely,
Yilei

*From:* Dong, Yilei 
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From 
the ReconAllDevTable here, *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
<https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>, 
do we structure the recon-all command to be: recon-all -autorecon2 
-fill -subjid ? I attempted to run recon-all -fill with -debug 
with the structure as follows: recon-all -s $subject -i $1 -fill 
-debug and I was wondering if this was the wrong format. I have also 
attached our recon-all-slurm-apr19.sb cluster submission file for 
reference.


Does recon-all -fill only run the fill step, while ignoring the 
previous steps before that or does recon-all run through all the 
initial steps including the -fill step ideally?


Regarding recon-all -debug, does the stdout file have the huge amounts 
of text specifying what each line is doing? I have included .out and 
.err files from the same recon-all -fill with -debug command for 
reference.


Sincerely,
Yilei

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly
not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will 
cause it to print out huge amounts of text specifying what it is doing 
on each line. You should also see if there is some stderr output that 
is not being caught. You can try running recon-all -fill on the 
subject that you created to see if the fill will run at all (this may 
be easier than waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our 
recon-all job submission script runs recon-all for 1 image. Given a 
folder of 100 MRI images, we have another script that calls upon the 
recon-all script for each image within the folder via a for loop. The 
result is 100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs 
are shared-node jobs, which means we run more than 1 job on a single 
node. This time, we increased RAM from 8GB to 16GB in hopes the 
entire recon-all processing stream can fully run through for each 
image, but it still stops at "mri_pretess done" and does not go on to 
the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 
28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all

Re: [Freesurfer] recon-all process still not finishing properly

[Dong, Yilei]

External Email - Use Caution

Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will just run 
the -fill step, do I submit it on the files that have already been run? In 
addition, does this error count as Freesurfer running out of RAM or it's more 
of a cluster issue I have to talk with the staff that manage it?

Sincerely,
Yilei

From: Dong, Yilei 
Sent: Tuesday, April 23, 2024 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all process still not finishing properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From the 
ReconAllDevTable here, 
https://secure-web.cisco.com/1lmfyKn6Pvakq-RQxgJbE5k4RDGG6d0Vpvb5lGcjzph3h7UE3rIOK94h4_vGK8oa4q_FYtrbTmYfXg9SF-sFCkj4DY_oUkqnlqG_VRr6zv-uPviunfO901Vr4Llra2RZoL7k2SaVz5b8sHZwz9tr28nK4K01ItC1QwtyMTw-gA6LKU-lK3jTTjAHXqq0NK-7yqLmD6TCtsqdbNsdoxGLEfnWyV4rlB4ypTtbp8RQCkTKa8EWWLysYONW6-m24iLcIBbOt0l9i4UxjEV-DHag-8gIkxA9SeCthGdnNmHPEyy8ngikQbSR5ckvogYu-nsAi/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable,
 do we structure the recon-all command to be: recon-all -autorecon2 -fill 
-subjid ? I attempted to run recon-all -fill with -debug with the 
structure as follows: recon-all -s $subject -i $1 -fill -debug and I was 
wondering if this was the wrong format. I have also attached our 
recon-all-slurm-apr19.sb cluster submission file for reference.

Does recon-all -fill only run the fill step, while ignoring the previous steps 
before that or does recon-all run through all the initial steps including the 
-fill step ideally?

Regarding recon-all -debug, does the stdout file have the huge amounts of text 
specifying what each line is doing? I have included .out and .err files from 
the same recon-all -fill with -debug command for reference.

Sincerely,
Yilei

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, April 18, 2024 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all process still not finishing properly

not sure what is happening. You can run recon-all with -debug and capture the 
output (both stdout and stderr) into a file. This will cause it to print out 
huge amounts of text specifying what it is doing on each line. You should also 
see if there is some stderr output that is not being caught. You can try 
running recon-all -fill on the subject that you created to see if the fill will 
run at all (this may be easier than waiting 4 hours).

On 4/8/2024 3:18 PM, Dong, Yilei wrote:

External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream never 
completely finishing.
We are still encountering the same problem. For context, our recon-all job 
submission script runs recon-all for 1 image. Given a folder of 100 MRI images, 
we have another script that calls upon the recon-all script for each image 
within the folder via a for loop. The result is 100 jobs running in parallel on 
the cluster.

I have attached a screenshot of the parameters we set whenever we submit each 
recon-all job for each image by SLURM to UCSD's cluster. The maximum time we 
are allowed for each job is 48 hours. Our jobs are shared-node jobs, which 
means we run more than 1 job on a single node. This time, we increased RAM from 
8GB to 16GB in hopes the entire recon-all processing stream can fully run 
through for each image, but it still stops at "mri_pretess done" and does not 
go on to the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.

If increasing the RAM did not change anything for us, how else can we get more 
verbose error messages? What other reasons could be why our recon-all aborts 
before finishing? I have attached a recon-all.log from one of our subjects for 
reference and a screenshot of the parameters we set for submitting jobs in our 
cluster for reference.


Freesurfer version: 7.2.0, but already available as module on UCSD's cluster 
system

Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Recon-all log: see attached


Thank you!


Sincerely,

Yilei



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1Pv7GW0cJEBRkDoNxnJuTO5eel1Em4ED-AsDRikPcYZfFw6NvllHzDdQK6OH4-hUM_5fxww8WdORdE6BgXd1_Kl6XnkSen7RhGQpAjqK34FdIcfEnxBuExdbuVGs-opQaCfmrzmpAfsPGtgwrZrtHxLHs1TicUxYbOTkF1w6HpJPI9xK_lVTXTFQi91WRvtgL46bbVfJHh3QF0i5U2qVsepG6pNCvRC_KfbEb-cBU67bHOQ5v7UPgvZlaeH6WVmJw8eTV8GPQvujReNCBnukpc7dCZdXRpyqsmqDSxuDT

Re: [Freesurfer] recon-all process still not finishing properly

[Dong, Yilei]

External Email - Use Caution

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From the 
ReconAllDevTable here, 
https://secure-web.cisco.com/168deFdRWVJ6rqWKdMIwjH_-sTPV9vncDkCBQheBnFXRjWPeM947jBmyBHJo3h-QEnDusTKbRmjjkTkDeDGvR3IZaeDV7vw2Td-KoOaXSRXub7gll1iS4zMc8ejCPJ3fNkbX-vkC_fosx5qsWn8IedW1Kr8lFwV1-6quZoijHC7oEiNozNkmbfREm-6mPo0f5RRuZBF1BESAsz2Hi-KrB3BeTh9VMEUOrbwcoMBVZMO7NH1LiT8XfJ0KeV_bWLPrB1HsW4d55bPQ8CwvSUWN8nVBmc5jKr3nYseN1h_SvY5PEFvJKmZ0GDgF9iTBaQ7P7/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable,
 do we structure the recon-all command to be: recon-all -autorecon2 -fill 
-subjid ? I attempted to run recon-all -fill with -debug with the 
structure as follows: recon-all -s $subject -i $1 -fill -debug and I was 
wondering if this was the wrong format. I have also attached our 
recon-all-slurm-apr19.sb cluster submission file for reference.

Does recon-all -fill only run the fill step, while ignoring the previous steps 
before that or does recon-all run through all the initial steps including the 
-fill step ideally?

Regarding recon-all -debug, does the stdout file have the huge amounts of text 
specifying what each line is doing? I have included .out and .err files from 
the same recon-all -fill with -debug command for reference.

Sincerely,
Yilei

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, April 18, 2024 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] recon-all process still not finishing properly

not sure what is happening. You can run recon-all with -debug and capture the 
output (both stdout and stderr) into a file. This will cause it to print out 
huge amounts of text specifying what it is doing on each line. You should also 
see if there is some stderr output that is not being caught. You can try 
running recon-all -fill on the subject that you created to see if the fill will 
run at all (this may be easier than waiting 4 hours).

On 4/8/2024 3:18 PM, Dong, Yilei wrote:

External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream never 
completely finishing.
We are still encountering the same problem. For context, our recon-all job 
submission script runs recon-all for 1 image. Given a folder of 100 MRI images, 
we have another script that calls upon the recon-all script for each image 
within the folder via a for loop. The result is 100 jobs running in parallel on 
the cluster.

I have attached a screenshot of the parameters we set whenever we submit each 
recon-all job for each image by SLURM to UCSD's cluster. The maximum time we 
are allowed for each job is 48 hours. Our jobs are shared-node jobs, which 
means we run more than 1 job on a single node. This time, we increased RAM from 
8GB to 16GB in hopes the entire recon-all processing stream can fully run 
through for each image, but it still stops at "mri_pretess done" and does not 
go on to the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.

If increasing the RAM did not change anything for us, how else can we get more 
verbose error messages? What other reasons could be why our recon-all aborts 
before finishing? I have attached a recon-all.log from one of our subjects for 
reference and a screenshot of the parameters we set for submitting jobs in our 
cluster for reference.


Freesurfer version: 7.2.0, but already available as module on UCSD's cluster 
system

Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Recon-all log: see attached


Thank you!


Sincerely,

Yilei



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/10vZ3lyKifsSsLtfZzgKvrT91yFm1-8drLKU54PSfnAnAiESmYS6W_CA2fgqhDO78xVRBn80uZ97W0Xc7Q10iR7JcW1W9ONn1KOEFSoWEDcvMesNEJvIXEvbI-bWho7fLs492h0mL1fjQ84GhzaBNBXvLOQFxJEmI8G5ZhJYg3m1BRxSytAaRVKW4ZxBCpj95Seq_GjOWjRncnVq-Jz2fycf9gxJxx_lTMM7AZtWP_1Qjb4cvPwgVoMlOhEGG_8SK6H3u6_BUfXAc6Xlrl6OrscdR2gE0eNXlwN08c3leIR5Bcj9bcYlhnnADh1y3alib/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1L9JtWIahKTHfxUVwdkxJIsmbw26B2aV-zoJtcXFvPFglatVfthNANOU6m6dINcqgOMcqNe6-NyaJ1AACvR352K7WfmeGGQLRHqelIETwyGo-Ax_nLddafs6AFMte7wozQAQA7-h9QiZAa9Y1ygaAONlIsaEVwAHq2B0Jk8QESmgqPwz4w_LSdAjkVLTuvd-sFzVsZcGTaW5j7FdAF9-lianwwSs1wX2pKmBJJeiImfx1uy946naVFPeEn9gh67Cbvtw25-pCSt2lspl0bliEpRlyxHBKqoO7SztH_LqXZyU506emutMUiW7URO2tyocR/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flist

Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will cause 
it to print out huge amounts of text specifying what it is doing on each 
line. You should also see if there is some stderr output that is not 
being caught. You can try running recon-all -fill on the subject that 
you created to see if the fill will run at all (this may be easier than 
waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


External Email - Use Caution

Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our recon-all 
job submission script runs recon-all for 1 image. Given a folder of 
100 MRI images, we have another script that calls upon the recon-all 
script for each image within the folder via a for loop. The result is 
100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs are 
shared-node jobs, which means we run more than 1 job on a single node. 
This time, we increased RAM from 8GB to 16GB in hopes the entire 
recon-all processing stream can fully run through for each image, but 
it still stops at "mri_pretess done" and does not go on to the -fill 
step. Each job submitted to the cluster took around 4 hours and 20 
minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 
15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Thank you!


Sincerely,

Yilei


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 .
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Re: [Freesurfer] Recon-all stuck at topology fix

[Fischl, Bruce R.,PHD]

Hi Salil

This looks like a T2-weighted volume. Recon-all by default assumes T1 
weighting. Do you have a T1 you can use (like an MPRAGE or FLASH scan)?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bhole, Salil
Sent: Thursday, April 11, 2024 12:36 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all stuck at topology fix


External Email - Use Caution
Here are some images from the patient. I also have the recon-all log posted 
here is well. This is the same patient but taken from a file where I tried to 
manually skull strip to fix the issue, however, the same issue persisted. Thank 
you for your help!

Best,
Salil

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: Wednesday, April 10, 2024 10:01 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all stuck at topology fix


* External Email - Caution *
Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the 
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce


On Apr 10, 2024, at 7:05 PM, Bhole, Salil 
mailto:bh...@wustl.edu>> wrote:


External Email - Use Caution
Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)


From: Bhole, Salil
Sent: Wednesday, April 10, 2024 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Recon-all stuck at topology fix

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)















The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

Re: [Freesurfer] Recon-all stuck at topology fix

[Fischl, Bruce R.,PHD]

Can you post some pictures? The norm.mgz, the wm.mgz, the lh.orig.nofix, the 
aseg.mgz, that kind of thing? Something is badly wrong….
Bruce

On Apr 10, 2024, at 7:05 PM, Bhole, Salil  wrote:



External Email - Use Caution

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)



From: Bhole, Salil
Sent: Wednesday, April 10, 2024 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Recon-all stuck at topology fix

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)








The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all stuck at topology fix

[Bhole, Salil]

External Email - Use Caution

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)



From: Bhole, Salil
Sent: Wednesday, April 10, 2024 5:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Recon-all stuck at topology fix

Hello,

I have tried to process this MRI a few times now and it always seems to get 
stuck on the step I have pasted below here. I have tried to fix the defect 
myself by editing the voxels manually, but that has also not seemed to help. 
I've looked through the MRI and there are no obvious deformities/defects. Any 
help with the next steps would be much appreciated.

Best,
Salil



49 defects to be corrected

0 vertices coincident

reading input surface 
/Applications/freesurfer/7.4.1/subjects/Ross_MRI_Neg_LITT/surf/lh.qsphere.nofix...

reading brain volume from brain...

reading wm segmentation from wm...

Reading original properties of orig.nofix

Reading vertex positions of inflated.nofix

Computing Initial Surface Statistics

  -face   loglikelihood: -8.8808  (-4.4404)

  -vertex loglikelihood: -7.5174  (-3.7587)

  -normal dot loglikelihood: -3.4734  (-3.4734)

  -quad curv  loglikelihood: -5.9156  (-2.9578)

  Total Loglikelihood : -25.7872

CORRECTING DEFECT 0 (vertices=116175, convex hull=11639, v0=288)








The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all exits with errors

[William Graves]

External Email - Use Caution

That worked beautifully. Thank you Yujing!

Best,
Will

On Apr 8, 2024, at 8:58 AM, Huang, Yujing  wrote:

It looks like mris_fix_topology for lh hemisphere core dumped. This is from 
your recon-all.log:

“
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see 
https://secure-web.cisco.com/1AL1TsrfyQOUqCIXXBqx1RFKat7TzQnns9gtsP_SH6wzu0JJzJkjPRGn3zXY_JKiXzmDUg1Nc-tzfFWQpnHPNPzMLf54XbW5rhuUGA5MICy0cmjt4T13DfL1WZ3UjjS63VM6tkZFUSUEoExarIh4A-bnUMdT6k2EqY8ke5fxffxSt6iXd9mdxqHflOb-HXLwwwWEWFIBhXuEGP7gqmxXBXQt4Y0PLDMHW5xXbd6p1UWbYRuAWsM8lTYDC8y_sGbrRGGh0BVYXqYffCWjcSBW9jo10Fn1RJv5Z3I0HoAee8hEl9ef5I-ThMyz6DUiUFYOZwobueqoJpKLo9-JDOmjv_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview
Large defect found - not a problem, but a curiousity
*** stack smashing detected ***: terminated
“

In the tutorial, it has instructions on how to correct topological defects.

Also, I noticed that the recon-all was run with ‘-parallel’ option. Use 
‘-nthreads ’ instead.

Best,

Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of William Graves
Sent: Sunday, April 7, 2024 10:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exits with errors


External Email - Use Caution

Dear FreeSurfer Developers,

I’m trying to run recon-all as a pre-processing step in the AFNI resting-state 
analysis pipline, using the command:
recon-all -subject $subj -i $anat_cm -all -parallel

So far it has successfully run on about 20 participants in my sample, but for 
the current participant it’s now suddenly throwing this error:

PIDs (691564 691567) completed and logs appended.
Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 
13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s R21-24 exited with ERRORS at Fri Apr  5 16:29:23 EDT 2024


I searched through the log file, tried Googling the error, and searched your 
email list archive, but couldn’t find anything to address this. The log file is 
attached, along with:

1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
2) Platform: Ubuntu 22.04.3 LTS

I’d appreciate any help or advice you could give!

Best,
Will

---
William W. Graves, Ph.D.
Associate Professor, Department of Psychology
Rutgers, The State University of New Jersey
Smith Hall, Room 337
101 Warren Street, Newark, NJ  07102
http://secure-web.cisco.com/1JFnzsz1va8MJlbUd3wgkrsTxdVUt375K3mHIHN6XQL6fWR6-LFIedc9AOZiELYuHWa0pzs4eLdlq8I3W9ahXVFxVLig0YsEv7t6rFeIqMtvR57RXU6jA0lBuyAIXcSxH8TKYvgWKx_iFt0cv39AmwSoX5tuaMPvFsE3JGj23OUUUGrFSQzWFdkm5iHLJQR4VL5txWBgm_BdmuTPwH3pwKX30lgFgTaAdXoEDpiYwV_tPdluo9TesEgepuUxHNJpq4apSlhUnXaWWdaeAKc_zJQaFJPVVPo92qLz3dtpdGlEgKvnVDaCVVoDj6SFZJZESw0T-MyWEM9X0wjySiHFnyQ/http%3A%2F%2Flbbil.rutgers.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at 
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Re: [Freesurfer] recon-all exits with errors

[Huang, Yujing]

It looks like mris_fix_topology for lh hemisphere core dumped. This is from 
your recon-all.log:

“
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
Large defect found - not a problem, but a curiousity
*** stack smashing detected ***: terminated
“

In the tutorial, it has instructions on how to correct topological defects.

Also, I noticed that the recon-all was run with ‘-parallel’ option. Use 
‘-nthreads ’ instead.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of William Graves
Sent: Sunday, April 7, 2024 10:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exits with errors


External Email - Use Caution
Dear FreeSurfer Developers,

I’m trying to run recon-all as a pre-processing step in the AFNI resting-state 
analysis pipline, using the command:
recon-all -subject $subj -i $anat_cm -all -parallel

So far it has successfully run on about 20 participants in my sample, but for 
the current participant it’s now suddenly throwing this error:

PIDs (691564 691567) completed and logs appended.
Linux demeter 6.2.0-26-generic #26~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Jul 
13 16:27:29 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s R21-24 exited with ERRORS at Fri Apr  5 16:29:23 EDT 2024


I searched through the log file, tried Googling the error, and searched your 
email list archive, but couldn’t find anything to address this. The log file is 
attached, along with:

1) FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
2) Platform: Ubuntu 22.04.3 LTS

I’d appreciate any help or advice you could give!

Best,
Will

---
William W. Graves, Ph.D.
Associate Professor, Department of Psychology
Rutgers, The State University of New Jersey
Smith Hall, Room 337
101 Warren Street, Newark, NJ  07102
http://lbbil.rutgers.edu
___
Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-All Clinical Stream: Image Output Observations in Creating ENIGMA QC Images

[Iglesias Gonzalez, Juan E.]

Dear Sam,
The native images live in one space (typically anisotropic), whereas the 
recon-all-clinical files always live in their own 1x1x1mm isotropic grid (which 
is the whole point!). I am not familiar with the Enigma QC procedure but I 
wouldn’t be surprised if it’s not compatible with these variable image spacings.
As a hack, you could maybe try running mri_convert native.mgz 
native.resampled.mgz -rl aseg.mgz, to obtain a (resampled) input scan in the 
same voxel space as the outputs?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sam Sievertsen 

Date: Friday, April 5, 2024 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-All Clinical Stream: Image Output Observations in 
Creating ENIGMA QC Images

External Email - Use Caution
Good Afternoon,

I hope this email finds you well! My name is Sam Sievertsen, the research 
coordinator for Dr. Jennifer Forsyth at the University of Washington. We are 
utilizing the recon-all clinical processing stream from FreeSurfer 7.4.1 on 
Rocky Linux (within our institutions HPC environment) to process subjects with 
decreased T1 image quality, and for whom previously processing with the 
standard recon-all pipeline resulted in missed grey matter during segmentation. 
Per recommendations in the bug reporting page, I have attached an example 
recon-all clinical log from this processing in case it is helpful.

Following the recon-all clinical processing of these subjects, we are using an 
existing (ENIGMA cortical QC) pipeline to take screenshots of the external 
cortical 
reconstruction
 / aparc+aseg segmentation overlaid on internal 
images.

We are able to successfully generate external (reconstruction) cortical QC 
images using the recon-all clinical output, but encounter an error when 
attempting to generate the internal (T1 with aparc+aseg.mgz overlay) QC images. 
Specifically, there is a conditional check within the internal QC image 
generation script linked above that halts the process if the Nx*Ny*Nz 
dimensions in the T1 image and the Nx*Ny*Nz dimensions in aparc+aseg.mgz do not 
align, which is where our process is throwing the error.

Manual examination of the recon-all clinical image output (e.g., "native.mgz", 
"synthSR.norm.mgz", and "aparc+aseg.mgz") suggests that the aforementioned 
dimensions are all different in those images. Conversely, the dimensions in the 
processed images and segmentations (e.g., "orig_nu.mgz", "aparc+aseg.mgz") from 
the standard recon-all pipeline appear to be uniform (256) for those same 
subjects we are processing in this cohort. To hopefully assist with clarity, I 
have attached the script we are using ("func_make_corticalpngs_ENIGMA_QC.m") to 
construct these internal QC images, and example output files from the same 
subject using the standard recon-all pipeline output 
("internalQC_standard_recon_all.txt") and recon-all clinical pipeline output 
("internalQC_recon_all_clinical.txt"), which show a discrepancy in the 
aforementioned dimensions.

Following up on the above information, I am wondering if "SynthSeg: to obtain a 
volumetric segmentation and linear registration to Talairach space"on the 
recon-all clinical 
page
 about registration to talairach space implies that the recon-all clinical 
output should have uniform dimensions, or if I am misunderstanding that and 
there is anything that stands out from this description that we may be doing 
incorrectly/that other users have encountered as well?

Would also be very appreciative o

Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

[Douglas N. Greve]

You have a space in your current path (between severe and similar). That 
is causing the problem


On 4/1/2024 8:26 AM, Huang, Yujing wrote:


There is a space in your path 
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.


Rename the directory name and try again.

Best,

Yujing

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *???

*Sent:* Sunday, March 31, 2024 11:18 PM
*To:* FreeSurfer 
*Subject:* [Freesurfer] recon-all mri_convert error: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")


*External Email - Use Caution *

Hello FreeSurfer Developers,

  I'm writing to ask for help while using "recon-all" command.

  I have converted some dcm format files to to nii format. Then I ran 
the command "recon-all -s maoyipeng -i 
first_sT1W_3D_TFE_tra_MR350895.nii -all", an error appeared:


/ mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii 
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz //
/mri_convert: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")/

/type mri_convert -u for usage/
/Command exited with non-zero status 1/
/@#@FSTIME  2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19/

/@#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19/
/Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux/
/recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 
2024 //


I've searched the list and didn't find a similar question. I'm a bit 
new to FreeSurfer, so I am unsure how to resolve this issue. I've 
attached the recon-all.log if that might help.


1) FreeSurfer 
version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP 
Wed May 24 00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

3) recon-all.log: see attached


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Re: [Freesurfer] recon-all mri_convert error: extra argument ("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")

[Huang, Yujing]

There is a space in your path 
‘/home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii’.

Rename the directory name and try again.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ???
Sent: Sunday, March 31, 2024 11:18 PM
To: FreeSurfer 
Subject: [Freesurfer] recon-all mri_convert error: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")


External Email - Use Caution

Hello FreeSurfer Developers,

  I'm writing to ask for help while using "recon-all" command.

  I have converted some dcm format files to to nii format. Then I ran the 
command "recon-all -s maoyipeng -i first_sT1W_3D_TFE_tra_MR350895.nii -all", an 
error appeared:

 mri_convert /home/pengcuiyi/Desktop/QinLab/MRI_human_brain/severe 
similar/first_sT1W_3D_TFE_tra_MR350895.nii 
/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz
  mri_convert: extra argument 
("/usr/local/freesurfer/subjects/maoyipeng/mri/orig/001.mgz")
  type mri_convert -u for usage
  Command exited with non-zero status 1
  @#@FSTIME  2024:04:01:09:09:04 mri_convert N 3 e 0.00 S 0.00 U 0.00 P 
100% M 5972 F 0 R 236 W 0 c 0 w 1 I 0 O 0 L 0.43 0.24 0.19
  @#@FSLOADPOST 2024:04:01:09:09:04 mri_convert N 3 0.43 0.24 0.19
  Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  recon-all -s maoyipeng exited with ERRORS at Mon Apr 1 09:09:04 HKT 2024

I've searched the list and didn't find a similar question. I'm a bit new to 
FreeSurfer, so I am unsure how to resolve this issue. I've attached the 
recon-all.log if that might help.

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b
2) uname -a: Linux ubuntu 5.4.0-150-generic #167~18.04.1-Ubuntu SMP Wed May 24 
00:51:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
3) recon-all.log: see attached


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Re: [Freesurfer] recon-all nu_correct error

[Dicamillo, Robert]

In our cluster testing, we allocate at least 16G to each recon-all command (see 
below).  We run about 150 of those commands in parallel on the cluster during 
off-peak usage and it takes about 12 hours for them to complete.

$ jobsubmit -A fsm -p basic -t 1-00:00:00 -m 16G "recon-all -all -s 0042 -I 
/path_to_subject_0042/001.mgz

The system requirements, 
https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements, stating 8G for 
recon all is intended for a users stand alone machine where memory is limited, 
there are no time/job resource limits - and so it might take 15 hours for a 
single recon-all to run.

- R.

On Mar 28, 2024, at 15:37, Dong, Yilei 
mailto:yid...@health.ucsd.edu>> wrote:

External Email - Use Caution

Hi Yujing,

For context, the way how I have the recon-all set-up is we have a recon-all job 
submission script that runs recon-all for 1 image. Given the folder of 100 MRI 
images, we have another script that calls upon the recon-all script for each 
image within the folder via a for loop. The result is 100 jobs running in 
parallel on the cluster.

I have attached a screenshot of the parameters we set whenever we submit each 
recon-all job for each image by SLURM to UCSD's cluster. The maximum time we 
are allowed for each job is 48 hours. However, my recon-all for all 100 
subjects takes on average 4.5 to 6 hours to run. Each image is also allocated 8 
GB of memory. Our jobs are also shared-node jobs, which means we run more than 
1 job on a single node.

Should we allocate more memory to each job than 8 GB or just reduce the number 
of jobs we submit at a time if 100 is a lot? We were able to successfully run 
through the entire recon-all for 5 subjects in parallel in the past.

Sincerely,
Yilei

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Thursday, March 28, 2024 11:53 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all nu_correct error

Hi Yilei,



I think "nu_correct: Command not found. FREESURFER: Undefined variable." is 
unrelated to your recon-all didn’t finish. That error happens in the beginning 
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct 
instead. We have addressed this error in our dev version.



I’m wondering if your cluster computer enforces some time, memory … limit on 
your job.



Best,



Yujing





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Dong, Yilei
Sent: Thursday, March 28, 2024 2:18 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] recon-all nu_correct error



External Email - Use Caution
Hi Freesurfer support,



Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's 
computing cluster. I get an error file that says "nu_correct: Command not 
found. FREESURFER: Undefined variable." I previously emailed this problem and 
was told to send my recon-all.log if running the recon-all did not work a 2nd 
time. I was also told previously that my cluster's Freesurfer can't locate the 
minc toolkit binaries on my system. How can this error be troubleshooted? 
Please let me know if you need any other information.



Freesurfer version: 7.2.0, but already available as module
Platform: Rocky Linux release 8.8 (Green Obsidian)
uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Recon-all log: see attached



Sincerely,
Yilei
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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] recon-all nu_correct error

[Huang, Yujing]

Hi Yilei,

I think "nu_correct: Command not found. FREESURFER: Undefined variable." is 
unrelated to your recon-all didn't finish. That error happens in the beginning 
of recon-all and recon-all uses ANTS N4BiasFieldCorrection for nu correct 
instead. We have addressed this error in our dev version.

I'm wondering if your cluster computer enforces some time, memory ... limit on 
your job.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dong, Yilei
Sent: Thursday, March 28, 2024 2:18 PM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all nu_correct error


External Email - Use Caution
Hi Freesurfer support,


Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's 
computing cluster. I get an error file that says "nu_correct: Command not 
found. FREESURFER: Undefined variable." I previously emailed this problem and 
was told to send my recon-all.log if running the recon-all did not work a 2nd 
time. I was also told previously that my cluster's Freesurfer can't locate the 
minc toolkit binaries on my system. How can this error be troubleshooted? 
Please let me know if you need any other information.



Freesurfer version: 7.2.0, but already available as module

Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 
UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Recon-all log: see attached



Sincerely,

Yilei
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

[Dan Levitas]

External Email - Use Caution

Thanks Yujing,

I realized that was likely the issue after sending my message. Indeed,
removing the -qcache option for this longitudinal processing step resolved
my issue.

Thanks for the clarification.

Dan

On Mon, Mar 25, 2024 at 9:37 AM Huang, Yujing 
wrote:

> The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base
> processing. So, I’m not sure that ‘-qcache’ option can be used in base
> processing.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Dan Levitas
> *Sent:* Thursday, March 21, 2024 11:56 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] recon-all mris_preproc error: Cannot find
> surf/lh.w-g.pct.mgh
>
>
>
> *External Email - Use Caution*
>
> Hello,
>
>
>
> I have a longitudinal dataset where each participant was scanned twice
> over the course of 5 months. I have been following FS's
> Longitudinal Tutorial
> 
> .
>
>
>
> For the CROSS section, each subjects' session scan successfully completed
> recon-all, where I used the following command:
>
> *recon-all \*
>
>
>
>
> *-subjid sub-${sub}_ses-${ses} \ -i $raw_anat_file   \ -qcache \ -all*
>
>
>
> I then used the following recon-all command for the BASE section:
>
>
>
>
>
>
> *recon-all \ -base sub-${sub}_year-1 \ -tp $subjects_dir/$pre_sub_ses   \
> -tp $subjects_dir/$post_sub_ses \ -qcache \ -all*
>
>
>
> This recon-all ran for several hours before failing at the following
> command:
>
> *mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target
> fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh*
>
>
>
> The error message is:
>
>
>
>
>
>
> *nsubjects = 1 ERROR: cannot find
> /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mgh
> Command exited with non-zero status 1 @#@FSTIME  2024:03:21:02:30:48
> mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M 3568 F 0 R 2201 W 0 c 2 w 45
> I 0 O 0 L 60.94 63.09 63.23 @#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc
> N 10 60.94 63.09 63.23 Linux c50.quartz.uits.iu.edu
> 
> 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64
> x86_64 x86_64 GNU/Linux*
>
> *recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48
> EDT 2024*
>
>
>
> I have checked the archive but can't seem to find a similar question. I'm
> a bit new to FreeSurfer, so I am unsure how to resolve this issue. I've
> attached the recon-all.log if that might help.
>
>
>
> *FreeSurfer version*:
> freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
>
> *Platform*: Red Hat Enterprise Linux 8.9 Ootpa)
>
> *uname -a*: Linux i48.red.uits.iu.edu
> 
> 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64
> x86_64 x86_64 GNU/Linux
>
> *recon-all log*: see attached
>
>
>
> Thank you.
>
>
> Dan
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/15JVDGWH0muukYX3WQqEohbfht0lDnSyO7hM-u-mwvB7BQuKYRCPkAbFe7GxIilghz8jSsynneTr0vkxX8IRZ00SJOIkeaXz8hkuR2Bc_ffsz0BX6NJLhSmWtiuqcd9luBHo2GSGRS3QNEcmLhD_vpFEZQMLfyCGNHgRiQ8l5gRqb0uca7QuUGivU_RBI41MzI0g_AH8Il8F4DtO149zG8pCy0hThlUiv8JtocO1MRR-v4jdPdZuODkZi25if4nYia-2nqVvYd2FwibSgstvD9ZjtO9KcnkbUtMim1wYXWwcTrjWa48gIh_5RLEc_k3Vw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigh

Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

[Huang, Yujing]

The recon-all ‘WM/GM Contrast’ step is skipped for longitudinal base 
processing. So, I’m not sure that ‘-qcache’ option can be used in base 
processing.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Dan Levitas
Sent: Thursday, March 21, 2024 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all mris_preproc error: Cannot find 
surf/lh.w-g.pct.mgh


External Email - Use Caution
Hello,

I have a longitudinal dataset where each participant was scanned twice over the 
course of 5 months. I have been following FS's Longitudinal 
Tutorial.

For the CROSS section, each subjects' session scan successfully completed 
recon-all, where I used the following command:
recon-all \
-subjid sub-${sub}_ses-${ses} \
-i $raw_anat_file   \
-qcache \
-all

I then used the following recon-all command for the BASE section:
recon-all \
-base sub-${sub}_year-1 \
-tp $subjects_dir/$pre_sub_ses   \
-tp $subjects_dir/$post_sub_ses \
-qcache \
-all

This recon-all ran for several hours before failing at the following command:
mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target 
fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh

The error message is:
nsubjects = 1
ERROR: cannot find 
/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mgh
Command exited with non-zero status 1
@#@FSTIME  2024:03:21:02:30:48 mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M 
3568 F 0 R 2201 W 0 c 2 w 45 I 0 O 0 L 60.94 63.09 63.23
@#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc N 10 60.94 63.09 63.23
Linux 
c50.quartz.uits.iu.edu
 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 
x86_64 GNU/Linux

recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48 EDT 2024

I have checked the archive but can't seem to find a similar question. I'm a bit 
new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the 
recon-all.log if that might help.

FreeSurfer version: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460
Platform: Red Hat Enterprise Linux 8.9 Ootpa)
uname -a: Linux 
i48.red.uits.iu.edu
 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 
x86_64 GNU/Linux
recon-all log: see attached

Thank you.

Dan

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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all command produces only 001.mgz file in the mri/orig directory

[Fischl, Bruce R.,PHD]

What was your recon-all command line? You need to give it a directive (like 
-all), otherwise it will just create a subject directory tree and put the 
001.mgz in the orig dir

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Naama Zur
Sent: Sunday, March 17, 2024 5:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all command produces only 001.mgz file in the 
mri/orig directory


External Email - Use Caution
Hi all,

I am using Ubuntu 23.1 with freesurfer 7.4.1 to run the recon-all command and 
the command runs without error and I do get a set of directories including: 
label, mri, scripts, stats, surf, tmp, touch, and trash. However, the only 
folders that are not empty are scripts where there are 11 files and  a 001.mgz 
file in the mri/orig directory.

I am not sure what I am doing incorrectly and was hoping for some guidance with 
this.

Thank you!
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Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

Hi Taylor,

I don't understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass 
full path to your rh.area and rh.area.pial.

What does 'mri_info rh.area' report?

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read 
access to rh.area


External Email - Use Caution
Hello FreeSurfer Developers,


I am attempting to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The recon-all.error file contains:

--
SUBJECT p03_8
DATE Tue Aug  1 15:58:13 EDT 2023
USER taylorariko
HOST C02F10PVPN5W.local
PROCESSOR x86_64
OS Darwin
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
/Applications/freesurfer/7.2.0/bin/recon-all
PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri
CMD vertexvol --s p03_8 --rh --th3

I have made sure that I have read, write, and execute access to the folder 
/path/to/subject/surf and the file rh.area. I can successfully run the command 
to make rh.area (mris_place_surface --area-map ../surf/rh.white 
../surf/rh.area), but the error persists in using rh.area. I have disk space 
and can run other commands such as this fake one (mris_calc -o rh.area.Test 
rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to 
rerun the command from root and get the same error message.

I found 2 similar threads of the mail-archive, though I didn't find any 
remedies:

  1.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.html
  2.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.html

Does anyone have any thoughts on how to trouble-shoot this? I have included my 
recon-all.log in the case it is of any use.


  1.  Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
  2.  Platform: macOS Sonoma 14.3.1
  3.  uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: 
Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64
  4.  recon-all.log: see attached


Thanks in advance!

Taylor Ariko

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The informatio

Re: [Freesurfer] recon-all-clinical synthseg error

[Agata Wolna]

External Email - Use Caution

Hi!

I've managed to debug the problem and it turns out that it was generated by
the mri_convert function - it produced a corrupted native.mgz image that
synthseg couldn't correctly read. I encounter this problem when pulling the
freesurfer:7.4.1 from dockerhub and when I was using a version downloaded
from the freesurfer website. Replacing the mri_convert script with a one
from a previous release (7.1.1) solved the problem, but I'm just letting
you know, in case that's a more general issue (and in all cases I was
running the script in a singularity containers).

Best wishes,
Agata

pon., 26 lut 2024 o 11:02 Agata Wolna  napisał(a):

> Hi!
>
> Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
> singularity container. What I did is to pull the freesurfer container from
> the DockerHub 
> (https://secure-web.cisco.com/171ahSlRX4vDMQD6prCFbKOWLRaTb3TeYqaUPEw1RHNCsVe3tGhp2kLFzWK3DJBLSx-UgUbpykn2uadM_p35sDDmGGUu-97iv7xWk1uOF7fCA5zzinTnVGh-ThVdtMXCb9wrWbtVUluLHZqPDir9P61Y41lyQx6J8ExkHyMN3nDhsdJG3NKQ0YCbHpN6OXcbMXy6k6AGFamQP8CZo_1lxhCV5WCZD26w_wkehvkhvpWl7Dd8-79VHNEEopR-cjICmGSqmg7GHDHiBc1SkoGDf-Hrij5PrwTlD6yLqb5U83FrN3wzFoW9dq-kjChSC2PKLUxnb8MKiKmHqCpn6WhL36g/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1)
>  and
> I replaced the /usr/local/freesurfer with this version:
> https://secure-web.cisco.com/1kTRkrixWgWU1iw8Qqe5X9q-Fz5Cs0dBxd03uelbVyK3aahbt-NDyUMFDpzSxsqPZKM2WUqoyOMnywfNkFMZP_5uzLcnYmhRlPJwt6eoOMbmo_-bFRvK9YV6H-tS6FGTlH7lZCDQw4Tr2_WlN4a-2ByEqPmRw_RHrKq8SU2Sk4aNDWHoS5lPwMqIs5td3Mpd2KWBbQCJ7f20xoIDdqxcxnMQ5K3m5nC2y5sS1QzfGMOTXHSLiC-7D-Dr218ggnoS6u3Eg-UqVFYGtZZm_ACvQ6OSAYJ7z7VdTRgX6PRuMv1mQLduPWJ1CXUv1RmUDCBI4mZKBJZd0GkBTpL_9yzF30w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
>  (build-stamp
> is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).
>
> Do you think that this might be an issue related to the differences in
> dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1
> with? Also, if you happen to have a containerized version of the newest dev
> version (or any version higher than 7.4, as I assume they would all support
> the recon-all-clinical function, right?) maybe I could just pull the entire
> container from somewhere and see if it solves the problem?
>
> Best wishes,
> Agata
>
> niedz., 25 lut 2024 o 21:56 fsbuild  napisał(a):
>
>>
>> It could help to know what OS version and what Freesurfer version you are
>> running.  From your path /usr/local/freesurfer it looks like you are
>> running a Freesurfer release, e.g.., 7.4.1.
>>
>> - R.
>>
>> On Feb 25, 2024, at 21:45, Agata Wolna  wrote:
>>
>> External Email - Use Caution
>>
>> Hi!
>>
>> I'm trying to run recon-all-clinical but I'm running into an error with
>> the SynthSeg at the very beginning. Do you have any hints what the problem
>> might be here? Here's the full error message:
>>
>> the following problem occured with image [mypath]/mri/native..mgz :
>> Traceback (most recent call last):
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in
>> predict
>> image, aff, h, im_res, shape, pad_idx, crop_idx =
>> preprocess(path_image=path_images[i],
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in
>> preprocess
>> im, _, aff, n_dims, n_channels, h, im_res =
>> get_volume_info(path_image, True)
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in
>> get_volume_info
>> im, aff, header = load_volume(path_volume, im_only=False)
>>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in
>> load_volume
>> x = nib.load(path_volume)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py",
>> line 110, in load
>> img = image_klass.from_filename(filename, **kwargs)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
>> line 503, in from_filename
>> return klass.from_file_map(file_map, mmap=mmap,
>> keep_file_open=keep_file_open)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
>> line 526, in from_file_map
>> header = klass.header_class.from_fileobj(mghf)
>>   File
>> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
>> line 171, in from_fileobj
>> + int(klass._data_type_codes.bytespervox[tp]) *
>> np.prod(hdr_str_to_np['dims'])
>> KeyError: 10
>>
>> resuming program execution
>>
>>
>> ERROR: some problems occured for the following inputs (see corresponding
>> errors above):
>> [mypath]/mri/native..mgz
>> Error in SynthSeg
>>
>> Best,
>> Agata
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>> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] recon all with optiBET brain mask

[BALBONI Irene]

External Email - Use Caution

Dear Yujing,
Thank you for your reply.  Would there be a way to just use the mask created 
with optiBET for the recon-all process to mask the brain? At the moment we are 
segmenting 2 images at once (mprage and mp2rage) to improve the quality of the 
segmentation and we have the skull-stripped images only for one of them so the 
solution below might not be ideal.

Thanks again.

Best,
Irene

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: venerdì 29 dicembre 2023 15:44
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon all with optiBET brain mask

This is from Freesurfer wiki - MailScanner has detected a possible fraud 
attempt from "secure-web. cisco. com" claiming to be https: //surfer. nmr. mgh. 
harvard. edu/fswiki/UserContributions/FAQ Q. I have already skull-stripped 
data. Can

This is from Freesurfer wiki -  MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1hcYnA9bt1-Vcu45hvleS0donbIaySbZpKWJuHfsnXO8nzzFMkFf6RlguN7q7Ki37PmP0BbVl5G4RMQxZvUItq3NuU1unMfgztpr902qkjmqcYuXGZyM1vwAy8R-sP9kEGQCrLt1i3cEJyhLhvrZA5Pnw2ti2KfIPuKQBLfhnmUNkm01pFq02N6h6mQbjsh3saIOfNKxSOBt0MhmKLXJMsWMeOm8mVzxqC5nvStkQZMayK7u5PhvIa53vXHUt-O-c4D6247GFmUoSPc-GlhRDRZPwIh84dqg-ZHQMdckTN11hW0XZIQ4BTBz624jJXZRz7nvEodQZ4SV50MPhK3_S7Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUserContributions%2FFAQ<https://secure-web.cisco.com/1tu630hE3EjDp_haYNYF6LD6KROQHLIzgLG2YW2r4AERBi9Le_GX2QSVu-x45Qv0YHxGYpACPN9wsvTACzaTa0f3R2lF49sUIzm_bvNOqHxZejuHRbadTG_BnhDr_s7O61j-x4qKWqUqQPPLVgawRh1SVUGMeTBhbuBzUE6FkTI0uAu8JE7KDMdnOM9-n4LOcoK9dsS7t2Tmx0uJgi-NsFmkAbNppylb2oc26pktuWeH-k5zm8epCnnHQ6yovd7CYq-3qL8ryed4kpvQBETYhvwpY4WpkVhue1Brn2CguSsPwmk5gu-5VyhNTxcOxnwvI6Rva7m3dxC1aWYWVqo_3QQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e1KlQ28-1bqlh2D9mdfR4oz5K2DcAapaDi_kIRYa9oOGpUGPN7HBgvT7nsrqBOhDSS1cOpeZ1vlmzNwZczc-cKlN2aymuKdjRBszVXj6pSIzy284SpTKycNB0Fu9kYvlF9WMrQLPBazYr7itkxhkOU3JWMD4-UoiVa9TbyhR71UonTZDQK57ox2IABmOi_Byg-ahMf7rWMa3NdavabkZhRt_6s9jZZE9ooyzXY-aFh0m-UBLCJJ5H-q_XO5-sie0nuzq8b8Z2HV6a3Q%2Fhttps*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FUserContributions*2FFAQ__;JSUlJSUl!!Dc8iu7o!yYcXtwVe5amhqAT_PYbjhL7D-Rul8VL7K6Hscbpi3nE-j2KdBG6QngAW5Xh4BwWedQvtXMFfGZeSzmxaAdZodUCCthFB$>
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 
Hope it helps.
 Best,
Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of BALBONI Irene
Sent: Tuesday, December 19, 2023 3:43 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon all with optiBET brain mask


External Email - Use Caution
Hello,

I would like to run recon all on a batch of subjects using 2 inputs (mprage and 
mp2rage). I would also like to run recon all using as brain mask not the 
standard brain mask generated by recon-all itself but a previously created 
optiBET. Would you have any suggestion on how to proceed? I tried simply 
replacing the brainmask file with the optiBET but it did not work.
Just for context all my participants (150) have been already segmented using 
recon-all but we noticed during quality control that we still have skull 
stripping and pial surface errors for the majority of them and that is why we 
would like to implement the optiBET mask.

Thanks for your help,
Irene Balboni
PhD student
She/Her

Institute de 
plurilinguisme<https://secure-web.cisco.com/1I_JnpDzyOEyx8Jc7K_q3g5IPB7KbXj-76l10Sg_ahaccSisgZ9e4iRurQRSsDvbTxAJ4xB1aUPEPKI_zZFEhxC76_IqIj2_J54iaGtEBmn3s20exzRYq6Kyi-0-HV6J5aypu0Zjn_ybfK34BZnCGYrStB1CN9gA67c7-nxePl9CW0m8oRFAimAy9xfsSd4-2AHkjffvE-6TaCMjfUWgkFzynqchCnkaQ2QOoasJTkMdcVGoVKYJpbubqx6lFduXwWsec74DTxrnBBQOg-VMbnEBcA0olXJ60rb1L_PRitAapjnHmwrfP8ja7FpPtja5VNnohaRQdWU76qufEXOhQNw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1pftPU5_0h0FupMF_jZDy_UxBYrJAQ-AW89umP7RzP_duHGk4rhiIzM9LB0z7YfOSEvpcpUW2Vvrg-ISqJbvImgtoneLSk8oyjNXZPhv9YQEwck2mFdw3ySjyETxvAv2nlmsAPBJkQ

Re: [Freesurfer] recon-all-clinical synthseg error

[Agata Wolna]

External Email - Use Caution

Hi!

Thanks for getting back to me. I'm running it on CentOS Linux 7 in a
singularity container. What I did is to pull the freesurfer container from
the DockerHub 
(https://secure-web.cisco.com/1mn_DXGJRkbRZaR60gIIXGTJuR-LMjZIaTJCeez5OyFU1R7CR20ybjGOUz4tzd1AxyLGwPEti0x8dbFUB84ln0O_02-s6U0uTIK8MKNSC2PQi8YfCoEy1p0wItYQUPIb5iUXIN6xmG1NisixJAmoRH2aeiF1Hp2ua8Vwv7N3sV2qz3yq-FulWe5CIozSDdVtKxL-8HDqKu5m6Qmq6GfHUwkb68AW0vPu6pVuINPmzlucZN1FMBI-oVzetjru-RxRd8CEUnQYS0kfVzJqg3J8RkaraRyC-2GgBwrxi-VPObQTTobQn8Ty4Vssycv8t2gGm0EGMq-eSNszHNtFSMXl9qw/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1)
 and I
replaced the /usr/local/freesurfer with this version:
https://secure-web.cisco.com/1VhsOWK6YuynPJZSTzGZep_xoqWFKijIbzVFTJkUW7wK3Iy1o63M730diiMYWK024Swr3mw9BBOIoTghZHgsLX-zhfP6VJWPQXHIZMmwb38t5iynLb8UTlDh2ES7braGKK28KbwDzrtuKHr6KKC__ikcHay2_nyeyuJS4IwgMAiqy9kk1c_jRMvKIvmNtHZnGGZHc2CGMi8aPtk5G4xQDteY56lAA64yYnRe_Lps-504c6Cz_3e4Nn8HCIblzADgs-Wd5j6sMe98DjAVApWr795qdo3M4CC3109D_5-l10o8bPlPWv6GeKT8TnmDAKUfThVbrpLKOB8jq9QJ6Pm1jmQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F
 (build-stamp
is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).

Do you think that this might be an issue related to the differences in
dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1
with? Also, if you happen to have a containerized version of the newest dev
version (or any version higher than 7.4, as I assume they would all support
the recon-all-clinical function, right?) maybe I could just pull the entire
container from somewhere and see if it solves the problem?

Best wishes,
Agata

niedz., 25 lut 2024 o 21:56 fsbuild  napisał(a):

>
> It could help to know what OS version and what Freesurfer version you are
> running.  From your path /usr/local/freesurfer it looks like you are
> running a Freesurfer release, e.g.., 7.4.1.
>
> - R.
>
> On Feb 25, 2024, at 21:45, Agata Wolna  wrote:
>
> External Email - Use Caution
>
> Hi!
>
> I'm trying to run recon-all-clinical but I'm running into an error with
> the SynthSeg at the very beginning. Do you have any hints what the problem
> might be here? Here's the full error message:
>
> the following problem occured with image [mypath]/mri/native..mgz :
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in
> predict
> image, aff, h, im_res, shape, pad_idx, crop_idx =
> preprocess(path_image=path_images[i],
>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in
> preprocess
> im, _, aff, n_dims, n_channels, h, im_res =
> get_volume_info(path_image, True)
>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in
> get_volume_info
> im, aff, header = load_volume(path_volume, im_only=False)
>   File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in
> load_volume
> x = nib.load(path_volume)
>   File
> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py",
> line 110, in load
> img = image_klass.from_filename(filename, **kwargs)
>   File
> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
> line 503, in from_filename
> return klass.from_file_map(file_map, mmap=mmap,
> keep_file_open=keep_file_open)
>   File
> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
> line 526, in from_file_map
> header = klass.header_class.from_fileobj(mghf)
>   File
> "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
> line 171, in from_fileobj
> + int(klass._data_type_codes.bytespervox[tp]) *
> np.prod(hdr_str_to_np['dims'])
> KeyError: 10
>
> resuming program execution
>
>
> ERROR: some problems occured for the following inputs (see corresponding
> errors above):
> [mypath]/mri/native..mgz
> Error in SynthSeg
>
> Best,
> Agata
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Re: [Freesurfer] recon-all-clinical synthseg error

[fsbuild]

External Email - Use Caution

 It could help to know what OS version and what Freesurfer version you are 
running.  From your path /usr/local/freesurfer it looks like you are 
running a Freesurfer release, e.g., 7.4.1.
- R.

On Feb 25, 2024, at 21:45, Agata Wolna  
wrote:External Email - Use 
CautionHi!I'm trying to run 
recon-all-clinical but I'm running into an error with the SynthSeg at the very 
beginning. Do you have any hints what the problem might be here? Here's the 
full error message:the following problem occured with 
image [mypath]/mri/native.mgz :Traceback (most recent call last):  
File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in 
predict    image, aff, h, im_res, shape, pad_idx, crop_idx = 
preprocess(path_image=path_images[i],  File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in 
preprocess    im, _, aff, n_dims, n_channels, h, im_res = 
get_volume_info(path_image, True)  File 
"/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in 
get_volume_info    im, aff, header = load_volume(path_volume, 
im_only=False)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", 
line 1377, in load_volume    x = nib.load(path_volume)  File 
"/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py",
 line 110, in load    img = image_klass.from_filename(filename, 
**kwargs)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py",
 line 503, in from_filename    return klass.from_file_map(file_map, 
mmap=mmap, keep_file_open=keep_file_open)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 526, in from_file_map    header = 
klass.header_class.from_fileobj(mghf)  File 
"/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py",
 line 171, in from_fileobj    + 
int(klass._data_type_codes.bytespervox[tp]) * 
np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some 
problems occured for the following inputs (see corresponding errors 
above):[mypath]/mri/native.mgzError in 
SynthSegBest,Agata___Freesurfer 
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Re: [Freesurfer] Recon-all Longitudinal Talairach issue

[Douglas N. Greve]

Can you send the recon-all.log file that contains the error?

On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:


External Email - Use Caution

Dear all,

I have run recon-all successfully on multiple subjects on multiple 
timepoints. If I open the mri folder, it shows the correct talairach 
files and no issues arose during processing.


However, when I then run the longitudinal pipeline (first base, which 
also shows correct files) on the subjects (recon-all -long SUBJXXtp1 
SUBJXXbase -all) the talairach shows an failure detection and the 
subsequent file is talairach.invalid.mgz.


The actual segmentation etc. seems fine when inspecting, but when I 
then want to run segmentBS.sh on these processed folders, it gives an 
error.


I have run this a few month back without issue, and had just a few 
subjects left, but now all of them show this same error. Any idea how 
this could be caused?


Kind regards,

Kirsten

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Re: [Freesurfer] recon-all ends prematurely without error

[Huang, Yujing]

Your recon-all command doesn't have the directive to tell it what to run - add 
option '-all' to your command.

See this wiki page for detail 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Weisholtz, Daniel S.,MD
Sent: Thursday, January 25, 2024 12:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all ends prematurely without error

Hello FreeSurfer team,

I have been using FreeSurfer for some time without difficulty, but I recently 
encountered a problem that I cannot overcome.  When I run recon-all using a 
command like this:

recon-all -s b047test -i 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz


the process terminates in just a few seconds without error.

The output reads as follows:
fs-check-version --s b047test --o 
/var/folders/44/ndjzqbx515991v_9vt0j8sprgq/T//tmp.IMS2K1
Thu Jan 25 12:35:02 EST 2024

setenv SUBJECTS_DIR /Users/danielweisholtz/Coregistration/subjects
cd /Users/danielweisholtz
/Applications/freesurfer/7.4.1/bin/fs-check-version --s b047test --o 
/var/folders/44/ndjzqbx515991v_9vt0j8sprgq/T//tmp.IMS2K1
-rwxr-xr-x  1 root  wheel  18565 Jun 14  2023 
/Applications/freesurfer/7.4.1/bin/fs-check-version

freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
$Id$
Darwin i.partners.org 21.6.0 Darwin Kernel Version 
21.6.0: Mon Aug 22 20:19:52 PDT 2022; 
root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64
pid 6977
Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
Subject does not have a bstampfile, copying 
/Applications/freesurfer/7.4.1/build-stamp.txt
Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
No constraints on version because REQ=UnSet and FsVerFile=NotThere
#@#% fs-check-version match = 1
fs-check-version Done
INFO: SUBJECTS_DIR is /Users/danielweisholtz/Coregistration/subjects
Actual FREESURFER_HOME /Applications/freesurfer/7.4.1
Darwin i.partners.org 21.6.0 Darwin Kernel Version 
21.6.0: Mon Aug 22 20:19:52 PDT 2022; 
root:xnu-8020.140.49~2/RELEASE_ARM64_T6000 arm64
/Users/danielweisholtz/Coregistration/subjects/b047test
\n mri_convert 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz
 /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz \n
mri_convert 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz
 /Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz
INFO: using NIfTI-1 qform
reading from 
/Users/danielweisholtz/Coregistration/raw/b047/b047_MRI_PreAx3DT1MPRAGE_July2022.nii.gz...
INFO: This is an unsigined short.
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to 
/Users/danielweisholtz/Coregistration/subjects/b047test/mri/orig/001.mgz...
~/Coregistration/subjects/b047test/mri/transforms 
~/Coregistration/subjects/b047test
~/Coregistration/subjects/b047test

Started at Thu Jan 25 12:35:02 EST 2024
Ended   at Thu Jan 25 12:35:06 EST 2024
#@#%# recon-all-run-time-hours 0.001
recon-all -s b047test finished without error at Thu Jan 25 12:35:06 EST 2024
done



The subject folder is created along with some of the files, but not much is 
actually there. I had been using FreeSurfer 7.2.0 but I upgraded to 7.4.1, and 
this did not resolve the problem.  Initially, I thought the problem was with 
the source file I was using, but I tested it with an MRI that I had previously 
used successfully with recon-all, and I got the same error. So something seems 
to have changed with my system that is causing this problem.

I am running FreeSurfer on a Mac using MacOS 12.6.

Many thanks for any assistance you can provide.

Sincerely,
Dan Weisholtz


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Re: [Freesurfer] recon-all cannot execute: required file not found

[fsbuild]

External Email - Use Caution

I don’t see what FREESURFER _HOME is set to, but if you used the .deb package 
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget 
 https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24
 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all 
queries ….,.. output deleted ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh … output deleted …
$ which recon-all
/usr/local/freesurfer/7.4.0/bin/recon-all
$ recon-all -version 
freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e
If you used the tar file instead, then some permissions might not be correct 
depending upon how/where it was unarchived (and some dependencies might be 
missing).
- R.

On Jan 19, 2024, at 15:20, Peled, Noam,PhD <npe...@mgh.harvard.edu> 
wrote:I'm just trying now to run the "recon-all -version", also without 
any arguments. Both produce the same 
error.Thanks!NoamFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing 
<yhuan...@mgh.harvard.edu>Sent: Friday, January 19, 2024 3:10 
PMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all 
cannot execute: required file not found I’m wondering how you ran 
recon-all.  Do you see the error even running it w/o any 
arguments? From: freesurfer-boun...@nmr..mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Peled, 
Noam,PhDSent: Friday, January 19, 2024 2:59 PMTo: Freesurfer support 
list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] 
recon-all cannot execute: required file not found Thanks Yujing,Yes, 
I looked for the file permissions using ls -l. It does have execute 
permissions.I also tried running chmod which didn't 
help.. Thanks,NoamFrom: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu>Sent: Friday, 
January 19, 2024 2:54 PMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all 
cannot execute: required file not found After sourcing Freesurfer, 
$FREESURFER_HOME is added to the front of your $PATH. 1. ‘ls -l 
$FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute 
permissions?2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the 
permission  Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On
 Behalf Of Peled, Noam,PhDSent: Friday, January 19, 2024 2:42 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
cannot execute: required file not found Dear group,I'm trying to run 
Freesurfer on digitalOcean server running Ubuntu 22.10 (GNU/Linux 
5.19.0-46-generic x86_64)I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)After sourcing 
Freesurfer, recon-all gives following error:.../freesurfer/bin/recon-all: 
cannot execute: required file not found Other functions, e.g. freeview, 
mri_info, all seem to work as expected Would love some 
help.Thanks,Noam  ___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

I'm just trying now to run the "recon-all -version", also without any arguments.
Both produce the same error.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 3:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


I’m wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



Thanks Yujing,

Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.

I also tried running chmod which didn't help.



Thanks,

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

I'm wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?

2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.

1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission


Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found

Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-all: cannot execute: required file not found

Other functions, e.g. freeview, mri_info, all seem to work as expected

Would love some help.
Thanks,
Noam


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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

External Email - Use Caution

 do not wish to continue communication over unencrypted e-mail, 

-Original Message-From:  "김민지" <minjik0...@kaist.ac.kr>To: 
"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>; Cc:Sent:  
2024-01-17 (수) 13:01:17 (UTC+09:00)Subject: Re: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

 do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" <hyejung7...@amc.seoul.kr>To: 
"Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error 
messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[김민지]

External Email - Use Caution

 do not wish to continue communication over unencrypted e-mail



-Original Message-From:  "윤혜정" To: 
"Freesurfer support list" ; Cc:Sent:  
2024-01-17 (수) 10:49:56 (UTC+09:00)Subject: [Freesurfer] recon-all errors 
(cannot execute binary file 
+External Email - Use 
Caution

Good day.

When I run recon-all for my nii files I get either one of the following error 
messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy 
setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error 
messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice mailto:hyejung7...@amc.seoul.kr

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Re: [Freesurfer] recon-all errors (cannot execute binary file +

[fsbuild]

External Email - Use Caution

It looks like you did not use the .pkg file installer to install Freesurfer on 
the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to 
use as FREESURFER_HOME.  The installer should ensure the privileges should 
be correct to run commands.   There are several 7.X freesurfer releases, 
but the latest release is 7.4.1 and you can download it via the link, e.g.,
https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19JuHE6WaWHssFDdzwRLVMRUHA3qj7h4ea64BhZk97t2IniNpnSEBUfevruwnZRT-WXrHBzlmbnxwfB-eUVqRKZYuKEwgZupdFOKnrwiz0xxPKw5DTxfL31t8mtljoZBWCtHjo8uXtSylGlGyZRzw2b6Kjz5JBf1zzrJTR_GSBoP7UPjKW3-cqENylh36UvAaYHpdFnPoZ4CrWPzQwkw7vmD7cmQcG6jBsy_w7nUkvkrhCZTYVfLg5BUluX8L0H85LGn_CikykHFVbAsE-L8Zih6Q9g6D25IvisceU2Rl_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
I would first remove what you have on your system from the terminal window with,
$ sudo rm -rf /Applications/freesurfer
Then in a Finder Window navigate to the Downloads folder (or to wherever you 
downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg).  You should be able 
to RIGHT CLICK on that file, select open with the default pkg installer, and 
then enter your password etc. to install it.  Right clicking should bypass 
having to do some of the security exemptions in system preferences.
Once the install is complete, setup the Freesurfer environment in the terminal 
window,
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects
MNI_DIR         
  /Applications/freesurfer/7.4.1/mni
You also need a license file, license.txt.  Once you complete the license 
request form 
at https://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC5od9QRlt9jwKuDUSQ6WtLlT9V17W1wUaBdznmlv7nMRbyPA6LYSYXyCAnP8F-Tuz_VE6STeVAxkh40QhJ8_Hz3w6xgC49SELup9uGscJnea_a5_YfPe4v_s5sGckdUErRUBLgOMN41ow4CikTKbC-IfUIre0ikhv0rLYF0iFjK9EZGFCuzHN7-z5cvA1mPBIjRTyGJsmV-behjR7Zpaho6a5uOuq1I4CB61WxtecgERQIEuY6PCEpMSMO1vfX-v7GEXY61w_SZ_5yg0kRQoolU2kwNaTPReDO7q7kH9B3AAFtRMPQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html%26nbsp;you
 will receive a file “licesne..txt” via the email address used in the form. 
  Download/copy the license.txt file to your machine from the email.
If your home directory is for example /Users/hyejung then you will see the 
following in the terminal window,
$ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung
… if you downloaded license.txt into your Download folder ...
$ cd Downloads$ ls license.txtlicense.txt$ cp -p -f  license.txt 
 $HOME/.$ cd $HOME$ ls license.txtlicense.txt
You could also use the Finder to navigate and drag/drop the license.txt into 
your home directory.   Once it it there, set the environment variable 
FS_LICENSE so freesurfer commands will find the license when they run,
$ export FS_LICENSE=$HOME/license.txt
Then it should work to run freesurfer commands from the terminal window 
including freeview.
- R.

On Jan 16, 2024, at 20:47, 윤혜정  
wrote:External Email - Use 
CautionGood day.When I run 
recon-all for my nii files I get either one of the following error 
messages:1. ERROR: could not configure recon-all parameters 
Killed 2. ERROR: could not configure recon-all 
parameters /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: cannot execute binary 
file /Applications/freesurfer/bin/fspython: line 20: 
/Applications/freesurfer/python/bin/python3: Undefined error: 0Or 3. a Pop 
Up message "_struct.cpython-38-darwin.so" cannot be opened because the 
developer cannot be verified. mac OS cannot verify that this app is free 
from malware. I googled the third error message and tried "Allow 
anyways" from the privacy setting. Then the next message pops up, 
then the next and the next. Could you please help me to understand the 
cause of the above 3 error messages? I tried to redownload freesurfer as 
well as python but none worked. Thank you in 
advance. Best,Alice___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

[Iglesias Gonzalez, Juan E.]

Dear Francesca,
Our method cannot reliably segment these thin/faint structures from clinical 
scans of arbitrary resolution and contrast, which is why they don’t get 
segmented.
If you want to segment the choroid plexus, you could take then intensities 
under the ventricles and split them into cerebrospinal fluid and choroid eg 
with optimal thresholding.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Biondo, Francesca 

Date: Friday, January 5, 2024 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

External Email - Use Caution
Hi,
recon-all generates these volumes, amongst others: “Left-vessel”, 
“Left-choroid-plexus”, “Right-vessel”, “Right-choroid-plexus”
recon-all-clinical does not generate these volumes. Or at least that I am able 
to detect. Any ideas how to extract or calculate them?

Regarding the choroid plexus, would it be correct to use this formula?
Estimated choroid plexus volume (both left and right) = “VentricleChoroidVol” – 
“left lateral ventricle” – “right lateral ventricle”

Thank you very much for your support -
Francesca

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Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[fsbuild]

External Email - Use Caution

  

Your Linux image could be missing system files and/or graphics card driver 
updates needed for the version of Qt included with Freeview to display graphics
 via X-Windows.  So I would first remove whatever currently exists under
 /usr/local/freesurfer and then follow the instructions on the Wiki page
 to do an install from scratch using the actual installer (instead of 
the tar file).  The instructions are here,



https://secure-web.cisco.com/1aVasdKo9Pwif5UQ2Uch0IDTvauLowJGIckrOUQbXQ2UgjMTijxM2AHRnYW5Sikm1PLFsVxTugqk7jS8q66aPC2Wt61zvugIk0ou082bvW2Vi2HpkhPUVK5RuQZz2bLaagNV35aRFc1BnYpdMMEOV_I7Kv2taVGg0rdW4UYbH_GJbhgkvI-Qa_RFQ4NdxHnAc16p7Z3HD0wL3Y4ADaC0Bqe1RvUwRo4c9f42ae38IHeHekPpYi9ZUSGHQmOdCa1fI-XUD5NHGSIodtj96CXK30LHfH3-4qIZuhpUMifnii45pKrnP74W9KNsZeK4DZQ5G5nnKr6Vfy1E4qFgc-u2-qw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu


After you install Freesurfer and setup the X-server on the Windows host -
 stop and verify basic graphics are working by running glxgears.  If 
communication from Linux running under WSL is working with the X-server 
on the Windows host, then you will see an X-Window open and display the 
spinning gears via the following Linux commands, 



$ sudo apt-get install mesa-utils

 answer Y to all prompts ... output deleted ...

$ which glxgears

/bin/glxgears

$ glxgears



The instructions on the wiki page end with running the "freeview" 
command with no arguments in order to test freeview can at least open 
and display an empty window.



If that works try displaying one of the volume files included in freesurfer,



$ freeview  $FREESURFER_HOME/subjects/bert/mri/brain.mgz



If that works, then try displaying one of your surfaces/volumes with your own 
freeview command.



If however glxgears worked, but the freeview command failed to open a 
window and/or display the volume as listed above, then the next step is to
 check for an upgrade to the OpenGL drivers on your Windows host.  
Freeview needs newer revisions of OpenGL in order to display graphics.  
Once you update the drivers, try running the freeview commands listed 
above again.



BTW - please remember to change SUBJECTS_DIR from 
$FREESURFER_HOME/subjects in your shell environment to a path your 
normal userid can write to w/o sudo/admin privs.  That could be in your 
home directory e.g.,



$ cd

$ mkdir subjects

$ export SUBJECTS_DIR=$HOME/subjects



You could put that export command in your shell init, e.g., $HOME/.bashrc file



- R.





On 1/6/24 13:25, Flemister, Abeoseh B. (flemist...@missouri.edu) wrote:






  
I’m using Ubuntu. 




Abeoseh Flemister

  

  
  From: Flemister, Abeoseh B. <flemist...@missouri.edu>

Sent: Saturday, January 6, 2024 12:24:40 PM

To: fsbuild <fsbu...@contbay.com>; freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
  

  


No, I installed using tar.gz





freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz










Abeoseh Flemister







From: fsbuild <fsbu...@contbay.com>

Sent: Friday, January 5, 2024 9:35 PM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Cc: Flemister, Abeoseh B. <flemist...@missouri.edu>

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 

 
Did you install Freesurfer 7.4.1 using the Debian installer package ?

https://secure-web.cisco.com/1IOiqTlEkTSd5OYr_A3naRtVr5L_K5zRpteC0_uUt7M0gRolNr7VK3lsQcU_qofF0IDf9if55xJELV6MPMHK0trMuv6brwoSd7MfQJKQ0u8rG6GpC55LrWIvHRVZ5RLVajCat58QdOxjxETxHox8d-pjPklYqzufhatlnoff9JNXFQBE2YZu1fSh7A_UI7FYF5ow5QHCaq4mgE4HIWjw_RKbxKvWi44qi3wAXyIcVfJoZw9W_iaRleXKYVjeCJHON3xsxb9jOhTdZWl0OJXUj8PIarGpr4vFjOdYhQu0_VBCO9368S1QeeP4BRzeKe2J-ZEzfrbiiNKrP3ru0vjOGZA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.



On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemist...@missouri.edu> 
wrote:



External Email - Use 
Caution



Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized. 



Abeoseh Flemister



From: fsbuild <fsbu...@contbay.com>
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Flemister, Abeoseh B. <flemist...@missouri.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 

 
For issues with Freeview displaying graphics when running
 via Linux on a Windows host thru WSL, you could look at the recent 
thread with the subject "Re: [Freesurfer] Freeview not showing output", 



https://secure-web.cisco.com/1KBH0OQxJdEKdxK38EEhCdBUjp55VUN1FBiZ5YthIc5pA61hlHgbL-cEwJvdn2C

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Flemister, Abeoseh B.]

External Email - Use Caution

I’m using Ubuntu.

Abeoseh Flemister

From: Flemister, Abeoseh B. 
Sent: Saturday, January 6, 2024 12:24:40 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

No, I installed using tar.gz

freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz<https://secure-web.cisco.com/1RPM72LVvQVxwxi2MWWpA9Rcm6cTLUAH8no49eYnQeNFUAbhBKjM9T8_HIKmZbTBn3OkeJCO6tBmlrvLRQAO5CVsIIDctoJffjQGzHJ0XvSKr_x_VnNimq-mwBGcP38jEJS433VTGjSQB6WTdnq375ISCDxFT3f1uT3V3zzB61wa3yR1Vqr4LelJdsP6A1QRIyCZkljxWlDMyv5oTMMRTOceDBmjTxDQoiEuI0RDtqQxcZrbZ60HAi0nSU0kObFAvxtmlBAZeAUIAfWJ2kJzSEjhQPkgjsiU5e8aZxye_FtFY0B9J5mVEqsS1hjcDnOqk/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz>

Abeoseh Flemister

From: fsbuild 
Sent: Friday, January 5, 2024 9:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Flemister, Abeoseh B. 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


Did you install Freesurfer 7.4.1 using the Debian installer package ?
https://secure-web.cisco.com/1HGKytO7fPBf6Lkw_Vs_mrlV6RgpJdmXBeCQxcgiUSj-liR5ThUq1ds21rhQvl1CrJNiGVXtBPvTxCHiq7wBtjlUAf7fqizarn-Wid1PxigtAYN4MIMoZ3kC2h9uNYd2_Q0L0HJfiReCPBHaD2DU7VVcQDv7X8AwijVNN24-WfALYapY7dGHMmLeLAI7sWkC40Cn8c-HkOJYro4olFppZYbqyM1SQKr2feMvi6CCSg3W1WIPZ-qm5PR7DMG3bBSUj2FWi_WedSD92pyK1gRK8fO5CYJFBINsZEiJA30SP__MMvWTvg5Fuayab3evOxTtF/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Jan 5, 2024, at 22:18, Flemister, Abeoseh B.  wrote:


External Email - Use Caution

Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized.

Abeoseh Flemister

From: fsbuild 
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Flemister, Abeoseh B. 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


For issues with Freeview displaying graphics when running via Linux on a 
Windows host thru WSL, you could look at the recent thread with the subject 
"Re: [Freesurfer] Freeview not showing output",

https://secure-web.cisco.com/1roW4eWJnbwwHlQRdZPkUpMIzTyiCES4FN2wNp4TeSNsoGVpv1cWD-6DpnAdEDvnXmIeaXS25RsYHNNZyzUMrPjiiJtO5cIwiw3wE7RrIs8phGwolm3Xf5RT7BrkzsnqqQSX4NgnxJA3VGEK9fONq2GHSY_6jNf3i6SAcivF5EqcwTvXFKr5-fbsn6aP9YoPoTsllh2E6wKcATv9GqiWXtK7SRwgXGIQhj-cOehv1UUHX9K4Zte38G-KjIhceNWE-PnqrHC-qXbTxgyMi0mjUr9VV_clWQlEQICmkfp48c5IHnM8KKTisX4KqFvtyt_4_/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html

In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,

https://secure-web.cisco.com/1liTVKOU80u8ktPNOWMfy7FxOOIFyhD6gPp4AOTyJKZfHXqK9KymyfkU2U6sQzXOQHyv9P9W5O2ZK41t44EGhEnP9qds_xDKyeWLBGt_esy2c5BvHkIRM6t7JzJN8NWJA3fqpvz3RJwJfMIxxItcdO3b1tXVp_ypRgnMX_L0g4VNcuIaNNKDp4K3NErXl4XADCEA0Mibs_Rg8XCAwmt2MqPG-C3K5AKMidrITwicW1skzJhckwdocwF3_XFLhs8Xw8I1MQWhXgRDVZEXzxmb5Vv1BQxH9k5mDYOkVV0cADbn0xLWb7w_6-0jpiFV9aKmk/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu

- R.

On Jan 5, 2024, at 21:08, Flemister, Abeoseh B.  wrote:


External Email - Use Caution

Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start because 
no Qt platform plugin could be initialized.

I saw an 
email<https://secure-web.cisco.com/1sex5BbjwVm7Vqn3F18BjMh4cio7IL8BUJJSNfISgMRjE97tPF6susbOp_EibTi_Rib1-3fWMGSEj8zGWHPxLR2GefWAJO6hAMhWk3ljFTJNt8UzJJ7g64luToLn5QhJsNduB0adfJnSocWm3Sr6UXIQTw_VG14v1_iXsFwciWl3tqZKsyg4XY7Bj1YRW5OCyZ_QQM_SNARfbprfL44uGWj3HS0vRM0ajIPDdJjRJEdjU_dtmR8Y7hdnowdnjN8MA7dH5ev7ZR64zoszVrlcknlcTe1L7BwLGzdSTIMvQRymZDCdDaTO7Ed60jgqgQZjr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66231.html>
 on this topic but I don't think it was ever answered.. Apologies if I'm 
reading the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
This is from your recon-all.log
“
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz



mri_convert: extra

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Flemister, Abeoseh B.]

External Email - Use Caution

No, I installed using tar.gz

freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz<https://secure-web.cisco.com/1i4fytfwvcgIlSWSAWWHQDmDh_-KYEw08gAGS3ODIYK6XhFyMeJv1V5W3aX7e5x6ccPhZhJScx-4XU9BPdika1UEbUXmPOkoLlLGCIQYqIVNJYxeGHtwjECdN2Hemm49R0J0zCsYPbPYm3gaHv4IyXscWMVzgTl0U8YjAezqxZiNmxSrEk3aE7fJj4mFYpxYMZJo2J-IsP1Ikk3cXzNAhKSF6knw2Hh4BA1dcP8WEXkwUY8PnCKviy62rtf1PjpdAF6ci0fpRW4Z0tcRcu9Ou4iy8ooFcslDUge8tQKneBb6qHkTPTjbwJcIO8JDNjVSRD-RLrQKq4cTojjhmwPfHuw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz>

Abeoseh Flemister

From: fsbuild 
Sent: Friday, January 5, 2024 9:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Flemister, Abeoseh B. 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


Did you install Freesurfer 7.4.1 using the Debian installer package ?
https://secure-web.cisco.com/1_pUSvIhWFfXZIWph9dfBK_bwLFppWgSeOhmjXxYr1T97RF5h1JwB402-ALfW4zXYeMS7s8Mk6r8_LTDcSNjUVdEqg3zqHPU3TuJ1h9hGJnTJN-8WHbos7IFeQEVmw_z_1BstBAfNQm1rkt-CgWKJFpgKKAfSUChKinLvZktq3dcALiL1BHsuuACMtVWCHPRHHM1kdlwb6yZYwhXP84bx7JxmrDjnEVkeYu_Jbx7fM7YmQgsVpaYpGwY71yVmWMBiIK9wT715U3z2lyC61sjXH1poR-Vrz5evo8qncdGngHBjRbvIdbcCL0AAt-8yHNEXLjnhiiG8swiJh3c2KuhFJw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Jan 5, 2024, at 22:18, Flemister, Abeoseh B.  wrote:


External Email - Use Caution

Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized.

Abeoseh Flemister

From: fsbuild 
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Flemister, Abeoseh B. 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


For issues with Freeview displaying graphics when running via Linux on a 
Windows host thru WSL, you could look at the recent thread with the subject 
"Re: [Freesurfer] Freeview not showing output",

https://secure-web.cisco.com/1bEDVzB9-yX2cTDOWGzLTkkafNvJNd2ARl1qFCBmhdZ2usAUb9EFYiq8Woy0DZ-B6NquMGfJbqTZqaQa_i7HXP99sjMY4QB1--i9QsbxQXdUFjAFg9MtyNYtjTrmmnQ4ub3V6PHNCRaE5dzR4dLaWswl2eg97UnUxRauVNvMF9K-DO4T2tnGjdNqKtcRYy9kK8vd-aPiZYB9PX7rXs5Mc6WvHWGjHwcKDec9kwUV5rwWFCUnEu3xhZmDzh1wHSwW3SxhLxZ2KW1kJWsYwqzXHHhognXV3t6LRV9MC9XG0_zIabNOcixFlyVJ5hqA2EuNhapNTfn1X6k1QGzuCxCFROg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html

In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,

https://secure-web.cisco.com/1X23V-5e4TVqi_z47ibkXrzpwR7MAqgwnbrWhV54F4jrSnt1WkHjTuFUIgbW-e0IroMCh-fQtlVJ9aDf5TXfwy5uZIh8ZrufKF_uMu4O8i0pc-00JQcl32TF9k8QMcPNJjl4BCaW6lpei_bUDHSxCE6ALmgvMaxstpSw7KPVY9mYgYCG25ad0deHAVH8tplXdYw95376PC6E-vx0xPt7sT_1q-1LcSbzuH54FLeiYuPC4pZdAzHLqZzN8TEU9xElqCsElu-oyGaZ8kRFiM8KkCJqSgyg-5nkR0erovr9GbuK_QteCfD2ik9Hmrb1bdNXrwiyYKvqSMtAoDgR7_CG9OA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu

- R.

On Jan 5, 2024, at 21:08, Flemister, Abeoseh B.  wrote:


External Email - Use Caution

Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start because 
no Qt platform plugin could be initialized.

I saw an 
email<https://secure-web.cisco.com/1sex5BbjwVm7Vqn3F18BjMh4cio7IL8BUJJSNfISgMRjE97tPF6susbOp_EibTi_Rib1-3fWMGSEj8zGWHPxLR2GefWAJO6hAMhWk3ljFTJNt8UzJJ7g64luToLn5QhJsNduB0adfJnSocWm3Sr6UXIQTw_VG14v1_iXsFwciWl3tqZKsyg4XY7Bj1YRW5OCyZ_QQM_SNARfbprfL44uGWj3HS0vRM0ajIPDdJjRJEdjU_dtmR8Y7hdnowdnjN8MA7dH5ev7ZR64zoszVrlcknlcTe1L7BwLGzdSTIMvQRymZDCdDaTO7Ed60jgqgQZjr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66231.html>
 on this topic but I don't think it was ever answered.. Apologies if I'm 
reading the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
This is from your recon-all.log
“
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz



mri_convert: extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
“



There is a space in your path to nii.gz.. Can you remove the space by renaming

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[fsbuild]

External Email - Use Caution

 Did you install Freesurfer 7.4.1 using the Debian installer package 
?https://secure-web.cisco.com/1Q45DaXEMcahL0g3wyejOntK1tGwx5UNQU25fdIi6ImofQsUOBUFGOhQ21vBk8sDRQfWWELU7ghl6F8QsJA6G2LpBun8SBG8VuebFtJaMobqrOERog6kz0hiKLV9ajDE2AKC1cpczWaDYkcSc4gMj3M6RFSGVTMvswdtfRVwJb-Ck23miRyGdEEMqm_Vf-b-J9o0O3vxunBYSB4cBN28DNJm4do5FWUZ4zSzRajltNg7RZ46COiMaso4uOBO2RYGe0GsZu0-WtJ9Aceq0QL43ZSK1SlxBsNnkMA4gJsKlawl_Tl3esT3lDUmN4303CUV1bHuzWMUv-G-vhN66uSWjhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb-
 R.
On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemist...@missouri.edu> 
wrote:External Email - Use 
CautionThanks, but the issue 
isn't that graphics aren't displaying, it's that freeview won't load because qt 
can't be initialized. Abeoseh FlemisterFrom: fsbuild 
<fsbu...@contbay.com>Sent: Friday, January 5, 2024 8:27 
PMTo: freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>Cc: Flemister, Abeoseh B. 
<flemist...@missouri.edu>Subject: Re: [Freesurfer] recon-all -s 
SiroSTC006_pre exited with ERRORS  For issues with Freeview 
displaying graphics when running via Linux on a Windows host thru WSL, you 
could look at the recent thread with the subject "Re: [Freesurfer] Freeview not 
showing 
output", https://secure-web.cisco.com/1oaJ0JSPhxlRjzZbZiQ7yaftYm3TvYL5vsUqSvRIwn1mxTLB9TJXbethBhfapiwejmtZvkPk-Rzn2z_ad008-CzQlNve-NK6CceUt0VtPPFJdwtHKP55BXcuQhcU1YMz4-FPp9GzSTpiJ3JHu0iWTdbP786ULqlSTxSVgPgP7VkSxFmOR08R6XsMAhtGAScfuIli7yeGgO6_pGTXQjtPhYf_rpwzgCC2fxaK-4G43kajshNd4Ud6bVNH54fIM-6dcft-18wReIbRAerhMZzSx7hql2Jiwn18OCmUKqAcP8rn9FrqtaYOtu1LGeBs5QWaxiqN9ZGDiVySHjpAlv-EeZg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.htmlIn
 case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link 
is,https://secure-web.cisco.com/1EiWtVy6tBY8avsFO7RwETRF3_M-X-xF2Kpa7qQsUO9MBq9hJVTqFCn_eb9DM39rNtk3pbFG-ug4ZpEKk6X5eQ2KDMDYdDUh5TpmffuF5wXtAdJ4hB-SoNLiV1Eby6E2JQ7J-CCBMpK3-i117c1ChJq3VJ47f5OEtaSJW1rpGX1NRsG3fz4fL7KgiZcAesTpPNIIbOF0oVPc7kQgLZgqih4rx94xTA9NBpzpd1HjHFBdtCE_iQGSw6wkenZH9UDB92x5b8fE-xVb2Lshe0GJ8hZ4FWXijzgb14x-T7Jq75dJgbZtGXjWNynrOPhOFqkTqD0jXb80ORfn3PZQGWxIN5g/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu-
 R.On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. 
<flemist...@missouri.edu> 
wrote:External Email - Use 
CautionHi Yujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start 
because no Qt platform plugin could be initialized.I saw an email on 
this topic but I don't think it was ever answered.. Apologies if I'm reading 
the thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing 
<yhuan...@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 
PMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORS WARNING: This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System.. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory? Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf 
Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORS External Email - 
Use CautionHi FreeSurfer 
Team, I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I saw a 
recent thread where someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.  I attached my 
reco

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Flemister, Abeoseh B.]

External Email - Use Caution

Thanks, but the issue isn't that graphics aren't displaying, it's that freeview 
won't load because qt can't be initialized.

Abeoseh Flemister

From: fsbuild 
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Flemister, Abeoseh B. 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


For issues with Freeview displaying graphics when running via Linux on a 
Windows host thru WSL, you could look at the recent thread with the subject 
"Re: [Freesurfer] Freeview not showing output",

https://secure-web.cisco.com/1MhQHLfqOsV0yN00hyLvm-y1m7NI9NP7S-GpPfeIKcao9Gurg-l-VxR3oFFgNMigTFOH5vpPTla3aaqG9EFYQLtkTcCypFCQi6-F9Aj6K-vJxzIVKdaq2yrn2d9_MVW_e1aZT99H34fjKatbjirW6RDrBVZu5gvhYZV275VPQHaZhSFpQHcotb8oxfG-rKiqe92eJQmxZcekLiIqe1b3I31pPffPJond76W6aRre-FXVp37VaJ21kdOV2QOLFm1PsMuIcXciYO60uk9o6Y9ljn_u7lyvyCXDrammj98BbGs7A_CJHAvk8GKKHee2q9gfPy6EAIhZXFLiJ6VPpRlwIaA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html

In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,

https://secure-web.cisco.com/1D77XANVVrjdkYfjYWX5qP542z7Dn3Frt2Qvbz-sr_9p66h5seQ9j96tnvd-97dZlpDJ2yyGFJbPCgi155qq3vN1Wj6bTb0MbHnIBi46tHc87Ykfy9MGdmOj2agrA49Tm5-Vu30ZcCoGJ43YHkzxTnEWOjte76l2mPHIph-RCH-zmBvMFj5Lq-sOEkF4nSO4BqfQuzo5LwopZUt8TYYu4jy33uwECNWBPGf9IgzRRFdJ24UlRspllchx3o0dTy1xV60O0cqS6ZQxL7EHJcVGq3t8ZO2RcqwucTIF-nyjJihYdht_hpeCOHtynTVgm9VLcM2q8ivjAPmTKBAMFeDuvDA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu

- R.

On Jan 5, 2024, at 21:08, Flemister, Abeoseh B.  wrote:


External Email - Use Caution

Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start because 
no Qt platform plugin could be initialized.

I saw an 
email<https://secure-web.cisco.com/1sex5BbjwVm7Vqn3F18BjMh4cio7IL8BUJJSNfISgMRjE97tPF6susbOp_EibTi_Rib1-3fWMGSEj8zGWHPxLR2GefWAJO6hAMhWk3ljFTJNt8UzJJ7g64luToLn5QhJsNduB0adfJnSocWm3Sr6UXIQTw_VG14v1_iXsFwciWl3tqZKsyg4XY7Bj1YRW5OCyZ_QQM_SNARfbprfL44uGWj3HS0vRM0ajIPDdJjRJEdjU_dtmR8Y7hdnowdnjN8MA7dH5ev7ZR64zoszVrlcknlcTe1L7BwLGzdSTIMvQRymZDCdDaTO7Ed60jgqgQZjr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66231.html>
 on this topic but I don't think it was ever answered.. Apologies if I'm 
reading the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
This is from your recon-all.log
“
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
“

There is a space in your path to nii.gz. Can you remove the space by renaming 
the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - 
/usr/local/freesurfer/subjects. You might run into permission or symbolic link 
problems later. It is a good idea to set SUBJECTS_DIR to some other directory 
where you have write permissions.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


External Email - Use Caution

Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ 
-all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all 
failed before completeing even the first step. I tried other files from our 
dataset and using .nii files and got the same result. I saw a recent thread 
<https://secure-web.cisco.com/1dNYuQ5feZYQ6hNc76goinSvD-Ypnc3onN5YQA8IZaGD9ZMsgPU8h02eq6smQW_JlVSoe2pmWi9i4IcVcvgPNAErLGWflT-2DHnEGZhHuYuSO7uagH4fed_iEleZMZ8fgVidAMFlNu_V6xq1SiHRk7nBL5_vNP6s-l8W5JP5TtFTlM7qsiZb0cfyjC0beae7q8RstHZ1a7H1bThMO8tUOdBPq6h2mtRu15a6hLnBK4v7YbPIeyWQj1PNy1poAzCsu_PpjvCs0OTiVKjJIHv6obmHjItvr-tP8RedoW0g4wzOQSCgST1rQnUsemz7IcLPP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg62253.html>
 where someone's issue was improperly labeled WM lesions but my dataset is 
composed of healthy brains.

I attached my recon-all.logs.. I am using a

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[fsbuild]

External Email - Use Caution

 For issues with Freeview displaying graphics when running via Linux on a 
Windows host thru WSL, you could look at the recent thread with the subject 
"Re: [Freesurfer] Freeview not showing output", 
https://secure-web.cisco.com/1_xzs3l0H18glGmrIaq7DLLWEnbalu4hRqRVJfIOVshijKYxcPt7YgAHaWtbElTSVhOHSVpXfVbYtsSat-VSB2AcASMfIu3iGWkg1Pr8PAWGiO-QNx_InTSbPx1SlEgEfWwHcu8Kvv6mpvP1DVjjMjrQm_tjS5mLYrxRY4oBZ9ZDYVcOJOgqZ1aNMNRZciur7DWeYIOQvMB3gIzoQ9Ezl_HmMYDUiQFPkcPHCm-jCkc9CwpFyswcD9oucICvpa2CcnjmJ_uKvLTTH3CMRECLNaxrDHkc_YoVNzJt4G1azbIURdLSwwIWcNW_J2fArM_PkVmgAJrH_G5HaO6Udtvukdw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76229.html
In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL 
above, that link is,
https://secure-web.cisco.com/1NIeWPFmWL9ULg_YLAREetdCKnwA4CAjtUSmmia-2fJLaumxUt7nyh4UJA8ETOUN9ZoOiTX5WwcajQ_sDAOOVJakF-Aqee8hi58icmc6NHSfROyRiZ5TQY-ecyB2kKnjaz0f3e5_Qg6RK-x6-rP_zvRBzKHU2gEyZgr8ivRTUzaCtcYqTpgdC7euLsajGvu0lgP3hQGs-pjDgQFqARk41W-gp9vVlFfkqZ7jqrzUHbXKJSgVrIz7OvWhnctAqDmu7vpLk74tAGnyrzsoRpHRX9TuybAZMwjHHOKh7_IVpBAwPkmQXb9UMnyrtgutVQ871ASnKlGXL3HfgSgCUITnwMA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FFS7_wsl_ubuntu
- R.
On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. <flemist...@missouri.edu> 
wrote:External Email - Use 
CautionHi Yujing,Thanks 
that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start 
because no Qt platform plugin could be initialized.I saw an email on 
this topic but I don't think it was ever answered. Apologies if I'm reading the 
thread wrong. Any help would be greatly appreciated!Abeoseh 
FlemisterFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing 
<yhuan...@mgh.harvard.edu>Sent: Friday, January 5, 2024 3:05 
PMTo: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with ERRORS WARNING: This message has 
originated from an External Source. This may be a phishing expedition that can 
result in unauthorized access to our IT System. Please use proper judgment and 
caution when opening attachments, clicking links, or responding to this 
email.This is from your recon-all.log“mri_convert 
/home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert:
 extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")“ There 
is a space in your path to nii.gz. Can you remove the space by renaming the 
directory? Also, your SUBJECTS_DIR points to your Freesurfer install 
directory - /usr/local/freesurfer/subjects. You might run into permission or 
symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some 
other directory where you have write 
permissions. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu
 <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf 
Of Flemister, Abeoseh B.Sent: Friday, January 5, 2024 3:31 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] recon-all 
-s SiroSTC006_pre exited with 
ERRORS External Email - 
Use CautionHi FreeSurfer 
Team, I am attempting to run recon-all on a 3T MRI image dataset. I used 
recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and 
recon-all failed before completeing even the first step. I tried other files 
from our dataset and using .nii files and got the same result. I saw a 
recent thread where someone's issue was improperly labeled WM lesions but 
my dataset is composed of healthy brains.  I attached my 
recon-all..logs. I am using a Linux virtual machine (FreeSurfer version 
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if 
you have any questions! Thanks,Abeoseh 
Flemister___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Flemister, Abeoseh B.]

External Email - Use Caution

Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve 
unfortunately run into another error: This application failed to start because 
no Qt platform plugin could be initialized.

I saw an 
email<https://secure-web.cisco.com/1sex5BbjwVm7Vqn3F18BjMh4cio7IL8BUJJSNfISgMRjE97tPF6susbOp_EibTi_Rib1-3fWMGSEj8zGWHPxLR2GefWAJO6hAMhWk3ljFTJNt8UzJJ7g64luToLn5QhJsNduB0adfJnSocWm3Sr6UXIQTw_VG14v1_iXsFwciWl3tqZKsyg4XY7Bj1YRW5OCyZ_QQM_SNARfbprfL44uGWj3HS0vRM0ajIPDdJjRJEdjU_dtmR8Y7hdnowdnjN8MA7dH5ev7ZR64zoszVrlcknlcTe1L7BwLGzdSTIMvQRymZDCdDaTO7Ed60jgqgQZjr/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66231.html>
 on this topic but I don't think it was ever answered. Apologies if I'm reading 
the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
This is from your recon-all.log
“
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
“

There is a space in your path to nii.gz. Can you remove the space by renaming 
the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - 
/usr/local/freesurfer/subjects. You might run into permission or symbolic link 
problems later. It is a good idea to set SUBJECTS_DIR to some other directory 
where you have write permissions.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


External Email - Use Caution
Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ 
-all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all 
failed before completeing even the first step. I tried other files from our 
dataset and using .nii files and got the same result. I saw a recent thread 
<https://secure-web.cisco.com/1dNYuQ5feZYQ6hNc76goinSvD-Ypnc3onN5YQA8IZaGD9ZMsgPU8h02eq6smQW_JlVSoe2pmWi9i4IcVcvgPNAErLGWflT-2DHnEGZhHuYuSO7uagH4fed_iEleZMZ8fgVidAMFlNu_V6xq1SiHRk7nBL5_vNP6s-l8W5JP5TtFTlM7qsiZb0cfyjC0beae7q8RstHZ1a7H1bThMO8tUOdBPq6h2mtRu15a6hLnBK4v7YbPIeyWQj1PNy1poAzCsu_PpjvCs0OTiVKjJIHv6obmHjItvr-tP8RedoW0g4wzOQSCgST1rQnUsemz7IcLPP/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg62253.html>
 where someone's issue was improperly labeled WM lesions but my dataset is 
composed of healthy brains.

I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer 
version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me 
know if you have any questions!

Thanks,
Abeoseh Flemister
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

[Huang, Yujing]

This is from your recon-all.log
"
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 
6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz 
/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

mri_convert: extra argument 
("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
"

There is a space in your path to nii.gz. Can you remove the space by renaming 
the directory?

Also, your SUBJECTS_DIR points to your Freesurfer install directory - 
/usr/local/freesurfer/subjects. You might run into permission or symbolic link 
problems later. It is a good idea to set SUBJECTS_DIR to some other directory 
where you have write permissions.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS


External Email - Use Caution
Hi FreeSurfer Team,

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ 
-all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all 
failed before completeing even the first step. I tried other files from our 
dataset and using .nii files and got the same result. I saw a recent thread 

 where someone's issue was improperly labeled WM lesions but my dataset is 
composed of healthy brains.

I attached my recon-all.logs. I am using a Linux virtual machine (FreeSurfer 
version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me 
know if you have any questions!

Thanks,
Abeoseh Flemister
___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon all with optiBET brain mask

[Huang, Yujing]

This is from Freesurfer wiki -  MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 
Hope it helps.
 Best,
Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of BALBONI Irene
Sent: Tuesday, December 19, 2023 3:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon all with optiBET brain mask


External Email - Use Caution
Hello,

I would like to run recon all on a batch of subjects using 2 inputs (mprage and 
mp2rage). I would also like to run recon all using as brain mask not the 
standard brain mask generated by recon-all itself but a previously created 
optiBET. Would you have any suggestion on how to proceed? I tried simply 
replacing the brainmask file with the optiBET but it did not work.
Just for context all my participants (150) have been already segmented using 
recon-all but we noticed during quality control that we still have skull 
stripping and pial surface errors for the majority of them and that is why we 
would like to implement the optiBET mask.

Thanks for your help,
Irene Balboni
PhD student
She/Her

Institute de 
plurilinguisme
 | Université de Fribourg
&
Brain and Language 
Lab
 | Université de Genève
c/o Campus Biotech
Chemin des Mines 9 – 1202
Université de Genève, CH
+41(0)223790141

Twitter
 | 
ResearchGate
 | 
Linkedin

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contains patient information, please contact the 

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

[James Hengenius]

External Email - Use Caution

Thanks for pointing that out! That seems to be working. Jim

On Thu, Dec 28, 2023 at 6:53 PM Huang, Yujing 
wrote:

> This is from Freesurfer wiki -
> https://secure-web.cisco.com/1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e1KlQ28-1bqlh2D9mdfR4oz5K2DcAapaDi_kIRYa9oOGpUGPN7HBgvT7nsrqBOhDSS1cOpeZ1vlmzNwZczc-cKlN2aymuKdjRBszVXj6pSIzy284SpTKycNB0Fu9kYvlF9WMrQLPBazYr7itkxhkOU3JWMD4-UoiVa9TbyhR71UonTZDQK57ox2IABmOi_Byg-ahMf7rWMa3NdavabkZhRt_6s9jZZE9ooyzXY-aFh0m-UBLCJJ5H-q_XO5-sie0nuzq8b8Z2HV6a3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUserContributions%2FFAQ
>
> *Q. I have already skull-stripped data. Can I submit it to recon-all?*
>
> A: If your skull-stripped volume does not have the cerebellum, then no. If
> it does, then yes, however you will have to run the data a bit differently.
>
> First you must run only -autorecon1 like this:
> *recon-all -autorecon1 -noskullstrip -s *
>
> Then you will have to make a symbolic link or copy T1.mgz to
> brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz.
> Finally, open this brainmask.mgz file and check that it looks okay (there
> is no skull, cerebellum is intact; use the sample subject *bert* that
> comes with your FreeSurfer installation to make sure it looks comparable).
> From there you can run the final stages of recon-all:
> *recon-all -autrecon2 -autorecon3 -s *
>
> Hope it helps.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *James Hengenius
> *Sent:* Thursday, December 28, 2023 5:06 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Recon-all failing with pre-skullstripped input
> data (mri_em_register can't find brainmask.mgz)
>
>
>
> *External Email - Use Caution*
>
> Hello FS experts,
>
>
>
> I downloaded some anatomical data. I have defaced full images and
> pre-skullstripped images for each participant. I tried the defaced images
> first, but FS skullstripping looks a little off (possibly because the
> defacing hides bits of the cranium in some images and causes problems in
> mri_watershed). So I would like to use the pre-skullstripped files as my
> initial inputs.
>
>
>
> I have placed the pre-skullstripped file for each participant in
> $SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input
> volume is named 001.mgz.
>
>
>
> I then submit the following command in a script to my slurm queue (after
> setting appropriate FS env vars), where the script input ${1} is the
> $subjid mentioned above:
>
>
>
> recon-all \
> -subject ${1} \
> -all \
> -openmp 40 \
> -noskullstrip
>
>
>
> The output log from FS ends with the following error. The
> function mri_em_register seems to be looking for brainmask.mgz, and fails
> to open it. If the input image is already extracted from the skull, do I
> need to manually call it brainmask.mgz rather than 001.mgz? Or am I missing
> something else in my function call (like order of flags)? Does
> -noskullstrip need to come before -openmp, for example?
>
>
>
> Thanks!
>
> Jim H.
>
>
>
> End of recon-all output:
>
>
>
> writing output to T1.mgz
> 3D bias adjustment took 1 minutes and 20 seconds.
> @#@FSTIME  2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P
> 128% M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22
> @#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64
> #-
> #@# EM Registration Thu Dec 28 16:08:25 EST 2023
> /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri
>
>
>  mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
> /home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca
> transforms/talairach.lta
>
>
> setting unknown_nbr_spacing = 3
> using MR volume brainmask.mgz to mask input volume...
>
>
> == Number of threads available to mri_em_register for OpenMP = 40 ==
> reading 1 input volumes...
> logging results to talairach.log
> reading
> '/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'...
> GCAread took 0 minutes and 1 seconds.
> average std = 7.2   using min determinant for regularization = 5.2
> 0 singular and 884 ill-conditioned covariance matrices regularized
> reading 'nu.mgz'...
> error:
>
> *mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz,
> -1): could not open file^@ error: mri_em_register: could not open mask
> volume brainmask.mgz. ^@*
> @#@FSTIME  2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P
> 118% M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64
> @#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64
> Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17
> 15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
>
>
> recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

[Huang, Yujing]

This is from Freesurfer wiki -  
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
Q. I have already skull-stripped data. Can I submit it to recon-all?
A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.
First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 
Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 
Hope it helps.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Hengenius
Sent: Thursday, December 28, 2023 5:06 PM
To: Freesurfer support list 
Subject: [Freesurfer] Recon-all failing with pre-skullstripped input data 
(mri_em_register can't find brainmask.mgz)


External Email - Use Caution
Hello FS experts,

I downloaded some anatomical data. I have defaced full images and 
pre-skullstripped images for each participant. I tried the defaced images 
first, but FS skullstripping looks a little off (possibly because the defacing 
hides bits of the cranium in some images and causes problems in mri_watershed). 
So I would like to use the pre-skullstripped files as my initial inputs.

I have placed the pre-skullstripped file for each participant in 
$SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input volume 
is named 001.mgz.

I then submit the following command in a script to my slurm queue (after 
setting appropriate FS env vars), where the script input ${1} is the $subjid 
mentioned above:

recon-all \
-subject ${1} \
-all \
-openmp 40 \
-noskullstrip

The output log from FS ends with the following error. The function 
mri_em_register seems to be looking for brainmask.mgz, and fails to open it. If 
the input image is already extracted from the skull, do I need to manually call 
it brainmask.mgz rather than 001.mgz? Or am I missing something else in my 
function call (like order of flags)? Does -noskullstrip need to come before 
-openmp, for example?

Thanks!
Jim H.

End of recon-all output:

writing output to T1.mgz
3D bias adjustment took 1 minutes and 20 seconds.
@#@FSTIME  2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P 128% 
M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22
@#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64
#-
#@# EM Registration Thu Dec 28 16:08:25 EST 2023
/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz 
/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca
 transforms/talairach.lta

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 40 ==
reading 1 input volumes...
logging results to talairach.log
reading 
'/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'...
GCAread took 0 minutes and 1 seconds.
average std = 7.2   using min determinant for regularization = 5.2
0 singular and 884 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
error: 
mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz,
 -1): could not open file^@
error: mri_em_register: could not open mask volume brainmask.mgz.
^@
@#@FSTIME  2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P 118% 
M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64
@#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64
Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17 
15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26 EST 
2023

For more details, see the log file 
/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log
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Re: [Freesurfer] recon-all error - MRISlabel2Mask()

[Douglas N. Greve]

yes, sending the full log file will be helpful. My guess is that the 
surfaces got out of synch (eg, if you had done edits).


On 11/21/2023 8:15 PM, Mark Wagshul wrote:


External Email - Use Caution

Dear Freesurfer experts,

Hi. Hoping someone can give me some guidance in how to proceed with 
this error in recon-all (at the moment, was running autorecon-wm, but 
not sure that’s relevant). Just pasting the last few commands which 
were successfully run, can send the whole recon-all.log file if 
needed. Nothing obvious in terms of the T1 or T2 images. Thanks!


#===

mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


Reading header for orig.mgz

Source registration surface changed to woT2.pial.rawavg

Target registration surface changed to woT2.pial.rawavg

7.3.2

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

srcsubject = sub-XXX

srcval = (null)

srctype    =

trgsubject = sub-XXX

trgval = woT2.pial.rawavg.conf

trgtype    =

srcsurfreg = woT2.pial.rawavg

trgsurfreg = woT2.pial.rawavg

srchemi    = rh

trghemi    = rh

frame  = 0

fwhm-in    = 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder = 1

UseDualHemi = 0

Reading source surface reg 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Loading source data

Reading surface file 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Applying linear registration transform

1.0 0.0   0.0  -0.4;

0.0 1.0   0.0   0.0;

0.0 0.0   1.0   0.3;

0.0 0.0   0.0   1.0;

INFO: trgsubject = srcsubject

Saving target data

/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



Tue Nov 21 17:49:18 EST 2023

#===

bbregister --s sub-XXX --mov orig/T2raw.mgz --lta 
transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc 
--proj-abs 1.5 --threads 1


tmp transforms/tmp.bbregister.3166191

Log file is transforms/T2raw.auto.log

Tue Nov 21 17:49:18 EST 2023

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


/public/apps/freesurfer/7.3.2/bin/bbregister --s sub-XXX --mov 
orig/T2raw.mgz --lta transforms/T2raw.auto.lta --init-coreg --t2 
--surf white.preaparc --proj-abs 1.5 --threads 1


bbregister 7.3.2

Linux cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu 
May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux


FREESURFER_HOME /public/apps/freesurfer/7.3.2

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

reading from orig/T2raw.mgz...

TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to transforms/tmp.bbregister.3166191/template.nii...

mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $

cwd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


cmdline mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

dof    6

nsep    1

cras0    1

ftol    0.000100

linmintol 0.01

bf   1

bflim 30.00

bfnsamp    30

SmoothRef 0

SatPct 99.99

MovOOB 0

optschema 1

Seed 53

Reading in mov transforms/tmp.bbregister.3166191/template.nii

Reading in ref brainmask.mgz

Reading in and applying refmask aparc+aseg.mgz

Setting cras translation parameters to align volume centers

Creating random numbers for coordinate dithering

Performing intensity dither

Re: [Freesurfer] recon-all error

[Huang, Yujing]

NaNs are in your original input image. They are replaced with 0 in the output 
mri/orig/001.mgz.

Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”. 
Is that your case?

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Alcocer
Sent: Tuesday, November 21, 2023 10:59 AM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all error


External Email - Use Caution
Reposting due to issue with email bouncing. I am receiving following error on 
my subjects. Recon-all still continues after error and finishes "without error" 
I have attached the recon-all log as well.

 mri_convert /path/to/inputt1.nii  /path/to/mri/orig/001.mgz

mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

Thank you,

Carlos


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Re: [Freesurfer] recon-all error

[Douglas N. Greve]

And how  did you create 001.mgz? Sometimes SPM will put NaNs in the 
image to indicate a mask.


On 11/17/2023 10:12 AM, Huang, Yujing wrote:


Hi Carlos,

Can you attach recon-all.log?

Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Carlos Alcocer

*Sent:* Thursday, November 16, 2023 4:57 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] recon-all error

*External Email - Use Caution *

Hi,

For some of my subjects I get the following error at the beginning of 
recon-all:


 mri_convert /path/to/inputt1.nii  /path/to/mri/orig/001.mgz


mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without 
error. What exactly is going on? This is only happens on some subjects.


Thank you,

Carlos


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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] recon-all error

[Huang, Yujing]

Hi Carlos,

Can you attach recon-all.log?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Alcocer
Sent: Thursday, November 16, 2023 4:57 PM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all error


External Email - Use Caution
Hi,

For some of my subjects I get the following error at the beginning of recon-all:

 mri_convert /path/to/inputt1.nii  /path/to/mri/orig/001.mgz

mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz
reading from /path/to/anat_t1.nii...
NaN found at voxel (0, 0, 244, 0)
error: No such file or directory
error: WARNING: 319676 NaNs found in volume /path/to/anat_t1.nii...

However, recon-all will keep running and then later finish without error. What 
exactly is going on? This is only happens on some subjects.

Thank you,

Carlos
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Re: [Freesurfer] Recon all clinical with multiple input scans

[Iglesias Gonzalez, Juan E.]

Dear Pauline,
Thanks for the interest in our new pipeline!
You can only run one scan at the time (but that scan may be of any resolution / 
contrast).
Cheers,
/E

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lieshout, P.B. van 
(Pauline) 
Date: Monday, November 13, 2023 at 03:51
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon all clinical with multiple input scans

External Email - Use Caution
Dear sir/madam,

I have been trying out the new recon-all-clinical algorithm. In the 
FreeSurferWiki on recon-all-clinical, it is not specified if I can add multiple 
scans (T1, FLAIR and T2, for instance) of the same individual in the 
recon-all-clinical command, similar to the old recon-all command. Is this 
possible in your new algorithm?

Thanks in advance,

Best,

Pauline van Lieshout



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Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

[fsbuild]

uot; <julian.con...@medma.uni-heidelberg.de>

Betreff: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error 
in SynthSeg


 

 

Besides
 patching the python distribution, another option available now is the 
development arm64 build for silicon Macs with an M1, M2 processor.  But 
this is not a release
 build and so has not been tested like a stable release.  The dev builds
 are currently ~3 months post the 7.4.1 release from back in June of 
this. year.  We’d be happy to hear how it goes if you try it.  The 
download links are below.


 


- R.





https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2QZ0blD-OpKmgogA7x9_rAfwfIcEGnZ7E8kgb9XNIzx2xLxQewJp32hJt31QUUAewAp1K7-Yjwk7lXCYxbaGdw8dtRE5zMFil4OqFhzHgZY7gNWOXHrgQ1zq6WrtnIl3Pllv0QaHc4JShUbdyQSVyQNgVymwLgj-PtjkDzhnise1J5RVUUczUi0PIoIHjn-dH5Ex7dw4_Tj8IUVRY1qDYHEdyBacN3YGVr6RlpLul0aH5727rGjfiCIau2iHg42KAJrBDTHZI1-iNSQ3tkbKJHbmkjy3X3wvfogE4XxSKFEkJaGyNNvit377-Ejbu0/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg

https://secure-web.cisco.com/1ISJip9DWoHbMeApDNRqD9f2lcyluijXFKQrQuGiqB8rzpImtFabgcaux9ndW9-G5RhmJNOcEQ9-gd-fykVbei9vIpDU6U6WOAGPq6mPgYiSQQoW2Px7Ob2Zo_FXId8Wx1NjQziQSpvypF0SdYASNSoHvjBlcM4teP8oQ389tlm8rAvEGeOyYjHTb9NxcM-FdqktYepdMb_AI7h0QYPhabKdLx7ov_zmUGt0DF-3KCJ-MxFWG_j5iPxQjdl_fbmnVILtM5TQEMRxhsEkVljqDwES3VUZmlJkR0Zrgekgl9LXYgMI3r8b_xbKEHB5nIhkyntGM3k1RD6bPsrH_VUDBosDDgqVZDHDBYGgsLFiI2ZY/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.tar.gz




 


 








On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel 
<asorby-ad...@mgh.harvard.edu> wrote:

 

External Email - Use 
Caution

 


Hi Julian,


 


I
 have managed to run recon-all on my Apple M1 macOS Ventura using the 
7.3.2 version of Freesurfer. It does not work on 7.4.2 or dev versions, 
however. These instructions were posted
 in a previous correspondence from fsbuild, but reposting here for 
anyone else having the same issue:


 


 


You may not be able to run these commands without sudo/admin permissions on 
your machine.



1) Download the tensorflow-2.4.1-py3-none-any..whl from,

MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=share_link





2) Check the download is OK with the md5 command in the terminal window,



$ md5 tensorflow-2.4.1-py3-none-any.whl

MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4



DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.





3) Setup the Freesurfer 7.3.2 environment (shown here as installed via 
..pkg file under /Applications) and verify the path to fspython is from 
the 7.3.2 release,



$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2

$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-darwin-macOS-7.3.2-20220803-878457d 

 environment variable settings output ...

$ which fspython

/Applications/freesurfer/7.3.2/bin/fspython





4) Uninstall the existing tensorflow package with,



$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow

 apart from any warnings you should see the output ...

Successfully uninstalled tensorflow-2.4.1





5) Install the package downloaded above.  This command assumes the package 
is in the current directory where the command is run.



$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install 
./tensorflow-2..4.1-py3-none-any.whl

 apart from warnings and output about requirements (which should all be 
satisfied) ...

 you should see tensorflow was updated .

Successfully installed tensorflow-2.4.1





CHECK THE UPDATE:



$ which fspython

/Applications/freesurfer/7.3.2/bin/fspython

$ fspython

>>> import sys, os

>>> import tensorflow

>>>



You should see the prompt return to ">>>" after the import 
of tensorflow with no errors reported.  Hit Ctrl-D to escape the 
python
 session.  The update should now be complete.






 


Once you have done this you should be able to run recon-all via 7.3.2. Hope 
this works!


Annabel


 




From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Iglesias Gonzalez, Juan E. 
<jiglesiasgonza...@mgh.harvard.edu>

Date: Tuesday, 26 September 2023 at 17:35

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction 
Error in SynthSeg

External Email - Use 
Caution

Dear Julian,


I believe this is a problem with
 SynthSeg not being compatible with the new microprocessor in MAC 
computers. Our software engineers are looking into solutions to this.


Sorry for the inconvenience,


E

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

[fsbuild]

External Email - Use Caution

 Besides patching the python distribution, another option available now is 
the development arm64 build for silicon Macs with an M1, M2 processor. 
 But this is not a release build and so has not been tested like a stable 
release.  The dev builds are currently ~3 months post the 7.4.1 release 
from back in June of this. year.  We’d be happy to hear how it goes if you 
try it.  The download links are below.
- 
R.https://secure-web.cisco.com/1aFiKh6YzbcJ_9V-mQth29TZB1SeCRdpmUdrLhAH6aMSmX5br3cwYdWzk2SQFt3E84yhkJiX8UK-RAuZILJgbwlYcKW-x-4lL7J9kQfLfOwFQG5-1tgyI_iripvurrqc6hOck5zgoIIIxfTjCln1LScJweoTJQieoYz1s4N4sXygNQqlfzYbhZ87LIW9VQGRj3pGteAMKpDrA0j70XQIZemwauVs7meaYj1FI3CZslQwLBeuOE_We0NCBttIsDNpUBA9GcXYMgvwYOvTrFJLWmtJC-RFpnOa99GI2QCrpNkkzMnpOxyTP4aWeg48D0LuNDHAP6kU4s-t48OHy1ayF1g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
https://secure-web.cisco.com/1M-Y1AHK0ybK-HgTbS6EGioPOtjnLKD9oxxiz5O9fG-v6vkulEnH6r0CCzH6_gqM7XnDt6h5dVioJARCFIs9drLzcnO1LHyzTb7WUdjqafmNknH1NK83adDrhak3Sn0exMT0arlACB6QxoPP0HHbD3XGSeh1J4lmUFtZL1p-3jhPqgbUtmG6BAvlnt3MD3uJupFP1_-m-dI9r4fGY_ENFKpEor-bOxOjnAEgsUMyTSBmNzqwbq1iJq7SVXWbbGEPMtKUzSaycRQ66l-WnTskj6bJ2pY1NVyvlLLVMcRl5MCn6pFnRIv9hh88VJ_fH706tE7zsAVUDgD3x6G_nVvYcbg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-macOS-darwin_arm64-dev.tar.gz


On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel 
<asorby-ad...@mgh.harvard.edu> 
wrote:External Email - Use 
CautionHi Julian, I have 
managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 version 
of Freesurfer. It does not work on 7.4.2 or dev versions, however. These 
instructions were posted in a previous correspondence from fsbuild, but 
reposting here for anyone else having the same issue:  You may not be 
able to run these commands without sudo/admin permissions on your machine.1) 
Download the tensorflow-2.4.1-py3-none-any.whl from,MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=share_link2)
 Check the download is OK with the md5 command in the terminal window,$ 
md5 tensorflow-2.4.1-py3-none-any.whlMD5 
(tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO NOT 
PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.3) Setup the 
Freesurfer 7.3.2 environment (shown here as installed via .pkg file under 
/Applications) and verify the path to fspython is from the 7.3.2 release,$ 
export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-darwin-macOS-7.3.2-20220803-878457d ... environment variable 
settings output ...$ which 
fspython/Applications/freesurfer/7.3.2/bin/fspython4) Uninstall the 
existing tensorflow package with,$ sudo 
$FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow... apart 
from any warnings you should see the output ...Successfully 
uninstalled tensorflow-2.4.15) Install the package downloaded above.  
This command assumes the package is in the current directory where the command 
is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install 
./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about 
requirements (which should all be satisfied) .. you should 
see tensorflow was updated Successfully 
installed tensorflow-2.4.1CHECK THE UPDATE:$ which 
fspython/Applications/freesurfer/7.3.2/bin/fspython$ fspython>>> 
import sys, os>>> import tensorflow>>>You should see the 
prompt return to ">>>" after the import of tensorflow with 
no errors reported.  Hit Ctrl-D to escape the python session.  The 
update should now be complete. Once you have done this you should be able 
to run recon-all via 7.3.2. Hope this 
works!Annabel From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, 
Juan E. <jiglesiasgonza...@mgh.harvard.edu>Date: Tuesday, 26 
September 2023 at 17:35To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] 
Recon-all-clinical error: Illegal instruction Error in 
SynthSegExternal Email - Use 
CautionDear Julian,I believe 
this is a problem with SynthSeg not being compatible with the new 
microprocessor in MAC computers. Our software engineers are looking into 
solutions to this.Sorry for the inconvenience,Eugenio --Juan Eugenio 
Iglesiashttp://http://secure-web.cisco.com/1DgebDH1WCLKceFhMcyIutLihRRkTXmu8dVOr_f4V0A6HCTGgJKyfIgRMdsGA0JY6XdTrwJ9fG9ZF0-rGeXJJR5xuIBa9pWzkJy1MlhajNkbUh4zQoyngk61Y8hRRh9IM13qb6kqn_EED7sD_b7NPGyxpBMu96UJ1F9G5j7HJMmMqjXAlpbHLU0UiAYP6rsxQW1ZwkHU2un5V_LBoaWBBc1MFIfXt_bJeLj_mRT0UANYNpBhXYIMiNEvjU8waDvcGl8LvssZu_7hBYMzrZ73aumJwKnWJdCaUAWrBMN6lK6lUpk3mvzSDFQ

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

[Sorby-Adams, Annabel]

External Email - Use Caution

Hi Julian,

I have managed to run recon-all on my Apple M1 macOS Ventura using the 7.3.2 
version of Freesurfer. It does not work on 7.4.2 or dev versions, however. 
These instructions were posted in a previous correspondence from fsbuild, but 
reposting here for anyone else having the same issue:


You may not be able to run these commands without sudo/admin permissions on 
your machine.

1) Download the tensorflow-2.4.1-py3-none-any.whl from,
https://secure-web.cisco.com/1klszb-du72zzOU81o6pWn28vjYMVSQcTmDSQ_1LxajxX2LGA-Qn7NWWyq4otvAYvgirpJZZwramc6xUHO2C1Sco6xEEPMLV5TsNecbtRMByuTaGB_p6LwlxMOIDDmgxpe_Ayf2p-nIhPny91tqK6kHa2L_AsKho73fNLGCNFsFm7yhjWRhHYS-3CluRtYkZWePoB-tkURZvGmhwzV4ENY_8MDUvUJTfxFZ9t-k5t-49gilwm_IcWpQZIFWuTEOga-GoVOxbvw9w8dXwhPWE-1yEQSY74iCf3nP7OntosrLk/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F15Qeve5FIA137KON67ehKIOyXy1N0PbAC%2Fview%3Fusp%3Dshare_link


2) Check the download is OK with the md5 command in the terminal window,

$ md5 tensorflow-2.4.1-py3-none-any.whl
MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4

DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.


3) Setup the Freesurfer 7.3.2 environment (shown here as installed via .pkg 
file under /Applications) and verify the path to fspython is from the 7.3.2 
release,

$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
... environment variable settings output ...
$ which fspython
/Applications/freesurfer/7.3.2/bin/fspython


4) Uninstall the existing tensorflow package with,

$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow
... apart from any warnings you should see the output ...
Successfully uninstalled tensorflow-2.4.1


5) Install the package downloaded above.  This command assumes the package is 
in the current directory where the command is run.

$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install 
./tensorflow-2.4.1-py3-none-any.whl
... apart from warnings and output about requirements (which should all be 
satisfied) ...
... you should see tensorflow was updated 
Successfully installed tensorflow-2.4.1


CHECK THE UPDATE:

$ which fspython
/Applications/freesurfer/7.3.2/bin/fspython
$ fspython
>>> import sys, os
>>> import tensorflow
>>>

You should see the prompt return to ">>>" after the import of tensorflow with 
no errors reported.  Hit Ctrl-D to escape the python session.  The update 
should now be complete.


Once you have done this you should be able to run recon-all via 7.3.2. Hope 
this works!
Annabel

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Date: Tuesday, 26 September 2023 at 17:35
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error 
in SynthSeg

External Email - Use Caution
Dear Julian,
I believe this is a problem with SynthSeg not being compatible with the new 
microprocessor in MAC computers. Our software engineers are looking into 
solutions to this.
Sorry for the inconvenience,
Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1Gpz43kiNknL9BKam5I7Djq85LOKVEn0-BDgYtOhgMCQJHuiwj-Za5vRUdJKZdPavOCSBV_POBXbo-JtObaxDBYc2zyZNSCWXV2u1rnluFwsXFJjjFfJgCqK1QsW6LWmh0V6vzP2AO_yPaw2XQxac7f1FAhNb-5PQqDBEViNWskat2B4H596Yc40XZZrkaP3Z2u_uuDHeKYhhHQ02vg-8vvGSBtrTqv3aG9CBqgaLSZVFpOMSPbdrc_BdgFbl9YgcKsxP5OyAUcWIpmjtXCnsjw/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Conrad, Julian 

Date: Tuesday, September 26, 2023 at 4:38 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in 
SynthSeg

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to  do a surface reconstruction from a GRE magnitude image using 
recon-all-clinical.sh
When I am running the pipeline, I get the following error:

Illegal instruction
Error in SynthSeg


neuroadmin@medma0236 ~ % recon-all-clinical.sh 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
 RC026_sub-010_ses-mri01 8 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer

#

#@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST



mri_convert 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz

reading from 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii...

TR=49.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.997386, 0.00125151, 0.0722456)

j_ras = (2.37011e-10, 0.99985, -0.0173204)

k_ras = (-0.0722564, 0.0172

Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg

[Iglesias Gonzalez, Juan E.]

External Email - Use Caution

Dear Julian,
I believe this is a problem with SynthSeg not being compatible with the new 
microprocessor in MAC computers. Our software engineers are looking into 
solutions to this.
Sorry for the inconvenience,
Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1RClgEwhBRH1QAsTAklfjXVf79ew6o_9qz3qIHu9I7VP3Ld8woAr9Sy2VIGiR_bbgGdbUN_DWwCF9X12OPeq0zvNV3O_jdzRnEewhHd0K5sIsGpmDybEVmOgMemJOQxtlVBdQaYHA-V0QLJ-4xaW6zcO6-CrzgXOqbAte7s_J535kGFb3Zw6PuLK39xIY8ucPZxjzav0SkUSB1ESXyZcZyJI63KpVMC6hjIWSZDy-Ki8YwhX_EsUP2Y_33P6Un8LPT3Lf_oRxCvl2rAYzvsHICA/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Conrad, Julian 

Date: Tuesday, September 26, 2023 at 4:38 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in 
SynthSeg

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to  do a surface reconstruction from a GRE magnitude image using 
recon-all-clinical.sh
When I am running the pipeline, I get the following error:

Illegal instruction
Error in SynthSeg


neuroadmin@medma0236 ~ % recon-all-clinical.sh 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
 RC026_sub-010_ses-mri01 8 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer

#

#@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST



mri_convert 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz

reading from 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii...

TR=49.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.997386, 0.00125151, 0.0722456)

j_ras = (2.37011e-10, 0.99985, -0.0173204)

k_ras = (-0.0722564, 0.0172751, 0.997236)

writing to 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz...



Illegal instruction

Error in SynthSeg

1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1
2) Platform: MacOS X Darwin

Hope this information is sufficient and there is an easy solution.
Best regards,
Julian

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The information in this e-mail is intended only for the person to whom it is 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all completed without error in 10 seconds

[Alan Francis]

External Email - Use Caution

Hello Lauren:

Open the sR0391178-0002-1-000208-01.nii.gz file using freeview and see
if the whole 3D brain is in place. This should give you a clue as to why
this occurred.

best,

Alan

On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens 
wrote:

> External Email - Use Caution
>
> Hi Freesurfers,
>
> I am attempting to run recon-all on a set of .nii.gz files.  Each file is
> in our subject directory and has run through recon-all.  Recon-all only
> takes 10 seconds to run and says it was completed without errors.  When I
> go to the folder recon-all creates, the folders are empty.
>
> Here is the code we ran:
>
> recon-all -s 967 -i
> /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz
>
> Here is the output message:
>
> Started at Wed Sep 13 10:52:44 PDT 2023
>
> Ended   at Wed Sep 13 10:52:54 PDT 2023
>
> #@#%# recon-all-run-time-hours 0.003
>
> recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
>
> done
>
> We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer
> version 7.3.2.
>
> I have attached the recon-all.log file and would appreciate any
> suggestions.  We have previously run many successful recon-all's and have
> not encountered any issues.
>
> Thank you,
>
> Lauren Stephens
>
>
> *Lauren Stephens, MS *
>
> Assistant Clinical Research Coordinator
>
> Department of Psychiatry and Behavioral Science
>
> *Stanford University School of Medicine*
>
> E: laure...@stanford.edu
>
> P: (650)-725-1716
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1FAb5I8xYlPAgBt9HJQcYvRJa1vFCwIguqkaqurJoq_3eDr9qIUVDzMBhzeBJOSXcT46BP83fIHRStZ5hk5A-MqjKtQsz-p-qxOFk_quW-9V0AJjPh21OwJM56-e1ZyXCMW77GBznDaM5uxMY5OatiT9p_5D_XvJsakBrfQBZie7kBfBLrl8blwYJEP11fIr8wl2N_xjJ1hSU2NEpxKaU-KPrjLiZMBNkbHLkUHU5Sbkn20B1xjTkjywsRKEWMsEGeNu_QyEdT-kpDfzOUUcvYL1T_6CsBErE1PheBQFEM6hTocEM5ntMidoi8QY97mwY02u24mFoINOu_yxrPtW_1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
___
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all completed without error in 10 seconds

[Huang, Yujing]

External Email - Use Caution

Hi Lauren,

You need to tell recon-all what to run. These are the options:

"
  Fully-Automated Directive:
-all   : performs all stages of cortical reconstruction
-autorecon-all : same as -all

   Manual-Intervention Workflow Directives:
-autorecon1: process stages 1-5 (see below)
-autorecon2: process stages 6-23
 after autorecon2, check white surfaces:
   a. if wm edit was required, then run -autorecon2-wm
   b. if control points added, then run -autorecon2-cp
   c. proceed to run -autorecon3
-autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ 
mri_seg)
-autorecon2-wm : process stages 15-23
-autorecon2-inflate1 : 6-18
-autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon
-autorecon3: process stages 24-34
   if edits made to correct pial, then run -autorecon-pial
"

Without passing one of options, I don't think it will run.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds


External Email - Use Caution
Hi Yujing,

Thank you, that did work!

Follow up question: Why would the code I used above, successfully generate the 
recon-all outputs for our other files?

Thanks,

Lauren Stephens




Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Wednesday, September 13, 2023 11:05 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds


External Email - Use Caution

Hi Lauren,



You will also need to specify '-all' to recon-all.



Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all completed without error in 10 seconds



External Email - Use Caution

Hi Freesurfers,



I am attempting to run recon-all on a set of .nii.gz files.  Each file is in 
our subject directory and has run through recon-all.  Recon-all only takes 10 
seconds to run and says it was completed without errors.  When I go to the 
folder recon-all creates, the folders are empty.



Here is the code we ran:



recon-all -s 967 -i 
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz



Here is the output message:



Started at Wed Sep 13 10:52:44 PDT 2023

Ended   at Wed Sep 13 10:52:54 PDT 2023

#@#%# recon-all-run-time-hours 0.003

recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023

done



We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 
7.3.2.



I have attached the recon-all.log file and would appreciate any suggestions.  
We have previously run many successful recon-all's and have not encountered any 
issues.



Thank you,



Lauren Stephens



Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716


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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all completed without error in 10 seconds

[Boa Sorte Silva, Narlon]

External Email - Use Caution

I think you need to pass the flag ‘-all’ in the command line.

recon-all -s 967 -i 
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz 
-all

Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon

On Sep 13, 2023, at 2:01 PM, Lauren Stephens  wrote:

[CAUTION: Non-UBC Email]
External Email - Use Caution

Hi Freesurfers,

I am attempting to run recon-all on a set of .nii.gz files.  Each file is in 
our subject directory and has run through recon-all.  Recon-all only takes 10 
seconds to run and says it was completed without errors.  When I go to the 
folder recon-all creates, the folders are empty.

Here is the code we ran:

recon-all -s 967 -i 
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz

Here is the output message:

Started at Wed Sep 13 10:52:44 PDT 2023
Ended   at Wed Sep 13 10:52:54 PDT 2023
#@#%# recon-all-run-time-hours 0.003
recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023
done

We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 
7.3.2.

I have attached the recon-all.log file and would appreciate any suggestions.  
We have previously run many successful recon-all's and have not encountered any 
issues.

Thank you,

Lauren Stephens

Lauren Stephens, MS
Assistant Clinical Research Coordinator
Department of Psychiatry and Behavioral Science
Stanford University School of Medicine
E: laure...@stanford.edu
P: (650)-725-1716

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continue communication over unencrypted e-mail, please notify the sender of 
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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all completed without error in 10 seconds

[Lauren Stephens]

External Email - Use Caution

Hi Yujing,

Thank you, that did work!

Follow up question: Why would the code I used above, successfully generate the 
recon-all outputs for our other files?

Thanks,

Lauren Stephens



Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Wednesday, September 13, 2023 11:05 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all completed without error in 10 seconds


External Email - Use Caution

Hi Lauren,



You will also need to specify ‘-all’ to recon-all.



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all completed without error in 10 seconds



External Email - Use Caution

Hi Freesurfers,



I am attempting to run recon-all on a set of .nii.gz files.  Each file is in 
our subject directory and has run through recon-all.  Recon-all only takes 10 
seconds to run and says it was completed without errors.  When I go to the 
folder recon-all creates, the folders are empty.



Here is the code we ran:



recon-all -s 967 -i 
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz



Here is the output message:



Started at Wed Sep 13 10:52:44 PDT 2023

Ended   at Wed Sep 13 10:52:54 PDT 2023

#@#%# recon-all-run-time-hours 0.003

recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023

done



We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 
7.3.2.



I have attached the recon-all.log file and would appreciate any suggestions.  
We have previously run many successful recon-all's and have not encountered any 
issues.



Thank you,



Lauren Stephens



Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu<mailto:laure...@stanford.edu>

P: (650)-725-1716


___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all completed without error in 10 seconds

[Huang, Yujing]

External Email - Use Caution

Hi Lauren,

You will also need to specify '-all' to recon-all.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Lauren Stephens
Sent: Wednesday, September 13, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all completed without error in 10 seconds


External Email - Use Caution
Hi Freesurfers,

I am attempting to run recon-all on a set of .nii.gz files.  Each file is in 
our subject directory and has run through recon-all.  Recon-all only takes 10 
seconds to run and says it was completed without errors.  When I go to the 
folder recon-all creates, the folders are empty.

Here is the code we ran:


recon-all -s 967 -i 
/Users/corpuscallosum/Desktop/subjects/sR0391178-0002-1-000208-01.nii.gz

Here is the output message:


Started at Wed Sep 13 10:52:44 PDT 2023

Ended   at Wed Sep 13 10:52:54 PDT 2023

#@#%# recon-all-run-time-hours 0.003

recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023

done

We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer version 
7.3.2.

I have attached the recon-all.log file and would appreciate any suggestions.  
We have previously run many successful recon-all's and have not encountered any 
issues.

Thank you,

Lauren Stephens



Lauren Stephens, MS

Assistant Clinical Research Coordinator

Department of Psychiatry and Behavioral Science

Stanford University School of Medicine

E: laure...@stanford.edu

P: (650)-725-1716

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

Recon-all-clinical worked consistently with 32 Gb RAM.  I used WSL Ubuntu
with 26Gb allocated to WSL before it would use swap.  I watched one run,
and it used total physical and swap memory of about 28 Gb.

With 16Gb RAM it worked on about 75% of scans.  I'm not sure why this
didn't work on some scans with 16Gb RAM and 100Gb swap space.  It would
crash around 23 Gb total memory usage.  I still wonder if there was some
configuration that would have allowed it to use more disk space as swap.


On Sat, Aug 19, 2023 at 10:45 PM fsbuild  wrote:

>
> Thanks for the updates.  Not that it will likely help with the memory
> underrun, but it should be straightforward to update Freesurfer from 7.2.0
> to 7.4.1 in the VM from the command line.
>
> You can use the Firefox browser in the VM to download the 7.4.1 installer
> with the link,
>
>
> https://secure-web.cisco.com/1qh9GqcyCJRYw9IPCV3zcxtF4nlkFXaGgUncXjaORpmG4FlI7I_HcpDNWptdiWcKMa25sAYzjBSikFGbJfaxjbE-WZ-vU1DmLifnHRpPyKe6cCk4hmu3rB2mWSJwaP45WRBwi6nHlkowPSy53LToGBR-vWBjPHwtpglCIrkdODGHkOKVjpOXIw3ulEc8sU06GOV4HG2tpFMAv8-OSD3ve-7d3Q0pNHnWnzQFKS5DbgpGEnbBOaeUH5jbMCMXJ96REnDA-OPmP-F72Fe3CuUfGFfXlD_2hzjVWmdxss1ViXxy4eFA_6uuvS203JGrzEChncGfyPjZbFXBs1FKygBxHFA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu18-7.4..1_amd64.deb
>
>
> In a terminal window, remove the existing freesurfer 7.2.0 installation,
> $ sudo apt remove freesurfer
>
> Then go to where the 7.4.1 installer was downloaded and run,
> $ sudo apt install ./freesurfer_ubuntu18-7.4.1_amd64.deb
>
> There was likely a soft link to the previous freesurfer distribution in
> developer's home directory, so to update that,
>
> $ cd $HOME
> $ rm -f  freesurfer
> $ ln -s  /usr/local/freesurfer/7.4.1  freesurfer
> $ ls freesurfer
> 
> ... check you have 7.4.1 ...
>
> $ cat  freesurfer/build-stamp.txt
> freesurfer-linux-ubuntu18_x86_64-7.4.1-20230614-7eb8460
>
>
> - R.
>
> On Aug 19, 2023, at 08:00, Matthew Lynch  wrote:
>
> External Email - Use Caution
>
> Thank you fsbuild for the suggestions.  Unfortunately it still does not
> work.  I did not try the virtual machine, because I could only find version
> 7.2.0 ova file on the freesurfer website.  It appears the 7.4.0 version
> does not yet have a virtual machine?  I am trying to use
> recon-all-clinical, which did not appear until 7.4.0.  The standard
> recon-all works fine on 1mm scans on my 16 Gb machine under WSL.  But I am
> trying to explore use of recon-all-clinical.
>
> It appeared as if WSL was not using any of the available swap space, so I
> tried a few different swap and memory configurations in .wslconfig.  Then I
> tried to create a cgroup that would limit physical memory and force
> freesurfer to use swap.  This did cause freesurfer to use swap space, but
> it still crashed with out of memory error when the combined swap and
> physical memory got to about 23 Gb (out of a total of 100 Gb virtual
> memory).
>
> I then created a total Linux version using Porteus Linux live USB and
> unpacking the freesurfer 7.4.0 tar.gz and finding a few minor
> dependencies.  This is a fairly lightweight Linux distro that runs from USB
> so I didn't have to create a dual boot.  The base memory usage was about
> 1.3 Gb before running recon-all-clinical.  I also activated a 16 Gb swap
> file with swapon.  It didn't work either, even in a pure Linux
> environment.  At maximum memory usage, it used only about 7-9% of the 16 Gb
> swap space and I think it also crashed at the same place around 21 Gb total
> memory usage with an OOM error.
>
> So it appears to be complaining of out of memory even when there is ample
> memory available in the form of swap space.  I have tried various options
> for vm.overcommit and vm.swappiness.
>
> This seems to occur only for a few selected scans.  For most of them it
> works.  There is a long error chain but this seems to be the relevant line:
>
> OOM when allocating tensor with shape[1,288,288,192,72] and type float on
> /job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu
> [[{{node model_5/unet_parc_merge_8/concat}}]]
>
> It fails there every time.
>
> I bit the bullet and bought an additional 16 Gb physical RAM for a total
> of 32 Gb.  I'll let you know if that works.
>
> On Sun, Aug 13, 2023 at 10:11 PM fsbuild  wrote:
>
>> You might be better off with swapping inside the Linux VM instead of on
>> the windows host.  Or I don’t see anything preventing the Windows host from
>> trying to swap out the entire VM process - which I would not expect to be
>> efficient.  You only need the application running *inside*the*Linux*VM* to
>> be swapped out if necessary (using the Linux OS to do that).
>>
>> This should be straightforward to setup using VirtualBox to run the
>> Ubuntu Linux VM we provide with Freesurfer already installed, i.e.,
>> download from
>>
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco

Re: [Freesurfer] recon-all-clinical out of memory error

[fsbuild]

External Email - Use Caution

 Thanks for the updates.  Not that it will likely help with the 
memory underrun, but it should be straightforward to update Freesurfer from 
7.2.0 to 7.4.1 in the VM from the command line.
You can use the Firefox browser in the VM to download the 7.4.1 installer with 
the 
link,https://secure-web.cisco.com/1NY_o7fEYkraJG0kPriDNOoRkAxLu_PnGwgYcRK1s8senK4bwr3tHkHxmqeA1ox3nv4eLHtKcyOszCYG2iNiDyCTypjVT3XBT4kycfC3LAaLKIWG_pEylRH9BHZQnOFmyrxU4noCzlrXuWiIR7PTEMvUVbduD-WGGg2rcqdN3MAN5iUlS-gfsCJyS0RLjqkERAU04kI2dcPPUE4qdvHhb21jI2n67gWL2EmGF-K8eCfEQRxuZsjeV_rYjPbqmbpbTkGuQRTcHfyLiaG4nAG6zCwrWdyy5UgeoP-u_COfxQZJw-siJZHD07V0nL0XMEkfscHmaOjEbQU8yA92IBEvCvA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu18-7.4.1_amd64.deb
In a terminal window, remove the existing freesurfer 7.2.0 installation,$ sudo 
apt remove freesurfer
Then go to where the 7.4.1 installer was downloaded and run,$ sudo apt install 
./freesurfer_ubuntu18-7.4.1_amd64.deb
There was likely a soft link to the previous freesurfer distribution in 
developer's home directory, so to update that,
$ cd $HOME$ rm -f  freesurfer$ ln -s  
/usr/local/freesurfer/7.4.1  freesurfer$ ls freesurfer
 
wrote:External Email - Use 
CautionThank you fsbuild for 
the suggestions.  Unfortunately it still does not work.  I did not 
try the virtual machine, because I could only find version 7.2.0 ova file on 
the freesurfer website.  It appears the 7.4.0 version does not yet have a 
virtual machine?  I am trying to use recon-all-clinical, which did not 
appear until 7.4.0.  The standard recon-all works fine on 1mm scans on my 
16 Gb machine under WSL.  But I am trying to explore use of 
recon-all-clinical.It appeared as if WSL was not using any of the available 
swap space, so I tried a few different swap and memory configurations in 
.wslconfig.  Then I tried to create a cgroup that would limit physical 
memory and force freesurfer to use swap.  This did cause freesurfer to use 
swap space, but it still crashed with out of memory error when the combined 
swap and physical memory got to about 23 Gb (out of a total of 100 Gb virtual 
memory).I then created a total Linux version using Porteus Linux live USB and 
unpacking the freesurfer 7.4.0 tar.gz and finding a few minor 
dependencies.  This is a fairly lightweight Linux distro that runs from 
USB so I didn't have to create a dual boot..  The base memory usage was 
about 1.3 Gb before running recon-all-clinical.  I also activated a 16 Gb 
swap file with swapon.  It didn't work either, even in a pure Linux 
environment.  At maximum memory usage, it used only about 7-9% of the 16 
Gb swap space and I think it also crashed at the same place around 21 Gb total 
memory usage with an OOM error.So it appears to be complaining of out of memory 
even when there is ample memory available in the form of swap space.  I 
have tried various options for vm.overcommit and vm.swappiness.This seems to 
occur only for a few selected scans.  For most of them it works.  
There is a long error chain but this seems to be the relevant line:OOM when 
allocating tensor with shape[1,288,288,192,72] and type float on 
/job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu[[{{node 
model_5/unet_parc_merge_8/concat}}]]It fails there every time. I bit the 
bullet and bought an additional 16 Gb physical RAM for a total of 32 Gb.  
I'll let you know if that works.On Sun, Aug 13, 2023 at 10:11 PM fsbuild 
 wrote:You might be better off with swapping inside 
the Linux VM instead of on the windows host.  Or I don’t see anything 
preventing the Windows host from trying to swap out the entire VM process - 
which I would not expect to be efficient.  You only need the application 
running *inside*the*Linux*VM* to be swapped out if necessary (using the Linux 
OS to do that).This should be straightforward to setup using VirtualBox to run 
the Ubuntu Linux VM we provide with Freesurfer already installed, i.e., 
download fromMailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1oFOJz1tXGspfsKNscw0jmPq8nuxBXOxbqTB1n-bwDnNM5mUz6pxVbABWcrVY94a9HN8Vx7byh5P0xNvKIFV8N1LW0Hu5cPXmnrNthADHDBuBRiRRp6d195GsQsDZDnJUej2pAr_nxobufSqEyZIhTg2JwjRrtPSmmd77hlBqEaGKfoFaUNBjQYj8gacvos_7DKkXlSOgQ_Ay5gbOgqdQPPEA6fPD8Bn4bYrf7667Fi4iVmRe66YRG32ggib0H07hOhTiyLOd2HIrDpDGnQ3GqJpRCFDHOvFfShQHILWzT-t_G-eXg7rn2Cwh4DvPZrYox56QeaEs6YybYELsOgFtVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67In
 the screenshot below, the FreeSurfer VM starts with 4G allocated to it.  
So correspondingly, inside the VM the “free” command reports there is ~4G 
available of which only 1G is being used s

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

Thank you fsbuild for the suggestions.  Unfortunately it still does not
work.  I did not try the virtual machine, because I could only find version
7.2.0 ova file on the freesurfer website.  It appears the 7.4.0 version
does not yet have a virtual machine?  I am trying to use
recon-all-clinical, which did not appear until 7.4.0.  The standard
recon-all works fine on 1mm scans on my 16 Gb machine under WSL.  But I am
trying to explore use of recon-all-clinical.

It appeared as if WSL was not using any of the available swap space, so I
tried a few different swap and memory configurations in .wslconfig.  Then I
tried to create a cgroup that would limit physical memory and force
freesurfer to use swap.  This did cause freesurfer to use swap space, but
it still crashed with out of memory error when the combined swap and
physical memory got to about 23 Gb (out of a total of 100 Gb virtual
memory).

I then created a total Linux version using Porteus Linux live USB and
unpacking the freesurfer 7.4.0 tar.gz and finding a few minor
dependencies.  This is a fairly lightweight Linux distro that runs from USB
so I didn't have to create a dual boot.  The base memory usage was about
1.3 Gb before running recon-all-clinical.  I also activated a 16 Gb swap
file with swapon.  It didn't work either, even in a pure Linux
environment.  At maximum memory usage, it used only about 7-9% of the 16 Gb
swap space and I think it also crashed at the same place around 21 Gb total
memory usage with an OOM error.

So it appears to be complaining of out of memory even when there is ample
memory available in the form of swap space.  I have tried various options
for vm.overcommit and vm.swappiness.

This seems to occur only for a few selected scans.  For most of them it
works.  There is a long error chain but this seems to be the relevant line:

OOM when allocating tensor with shape[1,288,288,192,72] and type float on
/job:localhost/replica:0/task:0/device:CPU:0 by allocator mklcpu
[[{{node model_5/unet_parc_merge_8/concat}}]]

It fails there every time.

I bit the bullet and bought an additional 16 Gb physical RAM for a total of
32 Gb.  I'll let you know if that works.

On Sun, Aug 13, 2023 at 10:11 PM fsbuild  wrote:

> You might be better off with swapping inside the Linux VM instead of on
> the windows host.  Or I don’t see anything preventing the Windows host from
> trying to swap out the entire VM process - which I would not expect to be
> efficient.  You only need the application running *inside*the*Linux*VM* to
> be swapped out if necessary (using the Linux OS to do that).
>
> This should be straightforward to setup using VirtualBox to run the Ubuntu
> Linux VM we provide with Freesurfer already installed, i.e., download from
>
> https://secure-web.cisco.com/1QjFp0WYmYLEMcfBOnXqbkQWZMeUHZaYYlKuZbGX26V8Vnk2ey_dREmr4sJ-WzYsL75GZjH-ZV4Oyk9pw_e5SHF4KorfUOcpPUi5hd8dgRWJrqz3KoWxCAC8Rj53KB1IZ9HkS-RBrl4YNlDQJofiV64p1CCKGaHFWQft2MxsVPSm27WyIvjTCzjO9ZkFYRXfd8lNO0US58QoJqtbxvKAbSp7zG4eV7PN01fZtOVLAw5m0ihpFXdKULLW-KPD-Xd1DR9-RgYjp4-IzqIj_aq859teaqgV0nLcfsnWLoQ9qSNHvCf7muxSmbzSzqdrbD7vk6LBOcvRIfWWTWRIbc2nA9w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
>
>
> In the screenshot below, the FreeSurfer VM starts with 4G allocated to
> it.  So correspondingly, inside the VM the “free” command reports there is
> ~4G available of which only 1G is being used since nothing consequential is
> running.  If you stopped the VM, increased the allocated memory in the
> VirtualBox application, and re-started the VM, you would see the total
> available memory scale up accordingly.
>
> For available swap space, you would look at the boot image on /dev/sda1.
> That image is made on purpose as small as possible so it can grow and/or
> space can otherwise be used.  The “df” commands shows that out of the box,
> the VM takes up 22G of the max allowed size of 170G.  That leaves
> potentially 170-22=148G to be used for other purposes.  You certainly would
> not want to allocate all that for swap space, but there is space to use for
> a good chunk of swap space apart from space you will consume doing work
> that adds files into the VM.   Here is 1 of many articles about setting up
> swapping in VirtualBox (which we do not setup by default),
>
>
> https://secure-web.cisco.com/1Q1M0ib1_obbWnUcE7Yr3awOIT-xkSxOF12MaXqwf5IIVtKXmy1WU9rMWC7GSXKQH2QEU0pJah9mpOKavuCNN4FuaflV410TS0w6_MqWJtt5Y-9rb1d6RRh-LsJKKoZkvUWpSwps1bwxQV5xpvapLwTd55X_s-DzyFok8qzxUPDCENCBnXNv8qCxZ0EUtrx1CF_nywimYKHCENTDFc_HTN7gNv1V7EGAUPKOKIAA6D38NO_zyvvNvopHdFbfME6HvgyN76YEymD-yNytqRuhY82x_nBhf9h1HGuCzL9lZ4TEl1JE4Im3XhG20-j--vHa_RIbkMzVK56-ZzEFptDGSlQ/https%3A%2F%2Fsciencetechvideos.wordpress.com%2F2019%2F01%2F09%2Fhow-to-add-swap-partition-or-swap-space-to-ubuntu-virtual-machine%2F
>
>
> The efficiency of swapping will be limited by your system, e.g.., how fast
> the disks are, their bus interface, etc.  There’s no guarantee even the
> most efficient 

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

The method I mentioned before does not always work.  It worked for all but
about 3 scans out of approximately 30.  There are some scans for which the
"committed memory" caps at about 23 Gb in the task manager and then either
the out of memory error occurs or the WSL session is killed.  Increasing
the .wslconfig swap and memory beyond 32 Gb didn't work.  Increasing the
Windows pagefile size to 8 Gb didn't work.  The output of free -h during
the synthseg run was 0Gb used, 40Gb free, which seems to suggest it is not
using the swap.  I suspect this is a matter of somehow getting WSL to
properly use large amounts of swap space.

On Thu, Aug 10, 2023 at 5:52 PM fsbuild  wrote:

>  Hello Matthew,
>
> Thanks for this info.
>
> If it is not too much work, just wondering if you could make a rough
> estimate or compute an average for the *total*memory* in use = (size of
> physical RAM in use by synthseg + size of all swap files resident on disk
> used by synthseg).
>
> - R.
>
> On Aug 10, 2023, at 16:08, Matthew Lynch  wrote:
>
> External Email - Use Caution
>
> Here is some additional follow up.  I was able to get recon-all-clinical
> working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and
> memory allowed in WSL..  This is done through the .wslconfig file which is
> located in the %USERPROFILE% folder (e.g. C:\Users\username\).  I had to
> specify a swap size of 32 Gb and also specify that WSL is allowed to use 32
> Gb (even though the system only has 16 Gb -- it will use swap space).
>
> Here is the .wslconfig file I used:
> -
> [wsl2]
>
> # Limits VM memory to use no more than x GB, this can be set as whole
> numbers using GB or MB
> # This must be set to 32 Gb or so to accomodate recon-all-clinical
> # If you set a 32 Gb swap but not 32 Gb memory allowance, WSL will stop at
> the memory limit and not use swap
> memory=32GB
>
> # Sets amount of swap storage space to 8GB, default is 25% of available RAM
> swap=32GB
>
> # Sets swapfile path location, default is
> %USERPROFILE%\AppData\Local\Temp\swap.vhdx
> # I believe the double backslash is necessary
> swapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx
> --
>
> For information on the .wslconfig file, see: *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1R9bbKcMD8m9Iba-TRQ62pSq0J_Ddg5C94ajqq7BXd_fbVgs6VGqnuPkYaI6ZDcu9NLaPE7lMDHy9lAzCrcphr6bsZLRFbQZzF4MWvRoR_PbphX012Jdo4VVUkclqw2EfcQDB717ZmZbfWgXfNRW-GPiUYqAakbNRgXJqa3wLU7OKD9gNyZXmuW_aISvDh2flGnHFq8HkqADXyypyekvureiTVE2TpURtac1BdduxYo18blHKpbaxn1kRWyPgpQATILi6AtheAZypd_rf4zg3tgSbdEC1qncpVovCwkRrQR3w-F4nTtVVflGTcBc_stqmABe_OjcVw0_B-uhAlpA92g/https%3A%2F%2Flearn.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl-config
> 
>
>
> On Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch 
> wrote:
>
>>
>> I was able to get recon-all-clinical working with 16 Gb computer.
>>
>> I thought the problem might be Windows hogging memory, so I created a
>> live persistent USB install of lubuntu, using lubuntu 22 as a low resource
>> distro in order to minimize memory usage, and installed freesurfer 7.4.0.
>> Even with initial memory usage on 1Gb on lubuntu, synthseg still failed
>> with out of memory error with 8 Gb swap file.  I watched the swap memory
>> fill up and then process was killed.
>>
>> I added 16Gb swap using the following instructions, for a total swap
>> space of 24 Gb + 16 Gb memory:
>>
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1jwI6G6GqqL8t7VhAFnki1fqPD46CaZzoct10KHE5JEIzVb2KnNMEPKOO9-sktJaM2kkvSg8-MY9svnsqbNsXpr444upYwiJRVoQzqgYy-595-LhU9OxZSjNEhUFkLqAnMWh_a-jpyL2Gfk86f34D45SbFUidGfjzbt2UpNnfTuOToHnTtU0Ul5OCA_IjUTF-49U2YHD8C2iVUpz0eJqPsfsJd-4NfX-ZcQUgcWroZxUMF2lJNze7OdaMrIEq6wnLn8SbWEfBxOYZ7LBfFO6CFvViSl72mH-i1gj2chNaoohZ6Dty90dFscxWgTS9mg8dWdBd-43B3VBQVsbQ4LTSCA/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-space
>> 
>>
>> This worked.
>>
>>
>>
>>
>>
>> On Thu, Jul 13, 2023 at 3:28

Re: [Freesurfer] recon-all-clinical out of memory error

[fsbuild]

External Email - Use Caution

 Hello Matthew,
Thanks for this info.
If it is not too much work, just wondering if you could make a rough estimate 
or compute an average for the *total*memory* in use = (size of physical RAM in 
use by synthseg + size of all swap files resident on disk used by synthseg).
- R.
On Aug 10, 2023, at 16:08, Matthew Lynch  
wrote:External Email - Use 
CautionHere is some additional 
follow up.  I was able to get recon-all-clinical working in Ubuntu in WSL 
on a 16 Gb machine by increasing the swap and memory allowed in WSL.  This 
is done through the .wslconfig file which is located in the %USERPROFILE% 
folder (e.g. C:\Users\username\).  I had to specify a swap size of 32 Gb 
and also specify that WSL is allowed to use 32 Gb (even though the system only 
has 16 Gb -- it will use swap space).Here is the .wslconfig file I 
used:-[wsl2]# Limits VM memory to use no more than x GB, this can be set as 
whole numbers using GB or MB# This must be set to 32 Gb or so to 
accomodate recon-all-clinical# If you set a 32 Gb swap but not 32 Gb 
memory allowance, WSL will stop at the memory limit and not use 
swapmemory=32GB # Sets amount of swap storage space to 8GB, default is 25% 
of available RAMswap=32GB# Sets swapfile path location, default is 
%USERPROFILE%\AppData\Local\Temp\swap.vhdx# I believe the double backslash is 
necessaryswapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx--For information 
on the .wslconfig file, see: MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1qV7qOd8MV8Me_H9OrBCSVXR30wzEoGDkBeHd3EGrM14KqAV3QgSA3NPSYDCQmZEjI3IBScWH0I4l3nd8okmiZxGDigkkrYLyO8vmtch63i9fBH9ADb6hgH46SuT2KDYJspHszp9mhrrl0AMgFv5b1aEUW-VSCZ5X5JL69gRnhCNObH2-vbK7kUXnwAoGnffh0nYmeZQ5Re955E7SWL6oJgkZwZaIyX5xF1dwo2Nud50cb69HJdnhAqFYounJ-eTXA4LdozmcTGz5xfnVs77f1JZNiDIvS7xIoHFrG8ttVhPjrCp84LTSa2LvsDKU4eXHgYCPpzg2pX6gA5WC_PsqWA/https%3A%2F%2Flearn.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl-configOn
 Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch  
wrote:I was able to get recon-all-clinical working with 16 Gb computer.I 
thought the problem might be Windows hogging memory, so I created a live 
persistent USB install of lubuntu, using lubuntu 22 as a low resource distro in 
order to minimize memory usage, and installed freesurfer 7.4.0.  Even with 
initial memory usage on 1Gb on lubuntu, synthseg still failed with out of 
memory error with 8 Gb swap file.  I watched the swap memory fill up and 
then process was killed.I added 16Gb swap using the following instructions, for 
a total swap space of 24 Gb + 16 Gb memory:MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to 
be https://secure-web.cisco.com/1eJ0r45kveGk81B9YYbQBd38RPcxAhW6yy1xCpY2JgWABNj1jDLYcbEOyK_mTjZs1jNOU9o8FFfx9J2BZHUQVHx5x-vTaCnVyovnc-nEXs5V3qZ30_38Dg0p9cACa5w1_lKVc9YpaDJACf-4L0hBx6QzEc11mvu9_ygulTf4O-h7dGx8IpranJ1pdCgtC0BBGATBsIsn1MLnoFMOtCXnGww8HwOTQOzCc1i2H__pxiCkp2tkzZLl_J3MCxPJYhNGotULIBJAy9k6io9RAiTaF41ibYapFMgPVpdzJgvqfgx7fns_Q3LIcKTEtM8lsc1yGd2_Tfr1j6EXuSsoOYb3PWg/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-spaceThis
 worked.On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch 
 wrote:I do not have access to a computer with 
more RAM.  I can run recon-all with 1mm T1 images without any 
problems.  How much RAM would recon-all-clinical be expected to 
need?  Does it require less RAM if it uses the GPU instead of 
CPU?  On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD 
 
wrote:External Email - Use 
CautionCan you try it on a 
computer with more 
ram?  From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Matthew LynchSent: Thursday, July 13, 2023 1:55 
PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] 
recon-all-clinical out of memory 
error External Email - Use 
CautionI am having trouble 
running the new recon-all-clinical module.  I input 5mm T1 axial DICOM 
images and it fails in SynthSeg with what appears to be an out of memory 
error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a computer 
with 16 Gb RAM.   Can anyone provide any thoughts on how to correct 
this?  Thanks in advance!  Here is the 
command: recon-all-clinical.sh ./T1AX5MM/119 fsclin 1  here is 
the error output: SynthSeg-robust 2.0using CPU, hiding all 
CUDA_VISIBLE_DEVICESusing 1 threadpredicting 1/1the following problem occured 
with image /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :Traceback 
(most recent call last):  File 
"/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in 
predict    post_patch_segmentation, post_patch_parcellation, qc_score 
= net.predict([image, shape_input])  File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

Here is some additional follow up.  I was able to get recon-all-clinical
working in Ubuntu in WSL on a 16 Gb machine by increasing the swap and
memory allowed in WSL.  This is done through the .wslconfig file which is
located in the %USERPROFILE% folder (e.g. C:\Users\username\).  I had to
specify a swap size of 32 Gb and also specify that WSL is allowed to use 32
Gb (even though the system only has 16 Gb -- it will use swap space).

Here is the .wslconfig file I used:
-
[wsl2]

# Limits VM memory to use no more than x GB, this can be set as whole
numbers using GB or MB
# This must be set to 32 Gb or so to accomodate recon-all-clinical
# If you set a 32 Gb swap but not 32 Gb memory allowance, WSL will stop at
the memory limit and not use swap
memory=32GB

# Sets amount of swap storage space to 8GB, default is 25% of available RAM
swap=32GB

# Sets swapfile path location, default is
%USERPROFILE%\AppData\Local\Temp\swap.vhdx
# I believe the double backslash is necessary
swapfile=P:\\Users\\username\\WSL\\wsl-swap.vhdx
--

For information on the .wslconfig file, see:
https://secure-web.cisco.com/1LNayjHy-1B5c1F-Uvbc7S2iZdU0Jv7SuKk5LkXsvEotEDyVYpDly5OU0naxoFLKh8oycxM1HnrZB2D3QAe7kjZO4VwUj0CV2ia_Ur93dhLdStO9YGvnPp1T8KYoYZ8A7SU_zjyQB9q9ZEi7XL01sOv12HVA3pEuB6kd3orUtCrIvisUeSzPIvYDMeUvcpq4A_uG1HjIF-fnvmVg9A33nNuNpSvIdykJz91NN-f-4LC9Bt6ltTemfRGXXDxenb-4_MKCs8ol-gZjauJ7RkwcbkGLcSMi3C9yY2H1aGvyG3PPWD7Nmgl0oaVF8XgRWUAjud_IN5AuL3R33m2S9TDJoYQ/https%3A%2F%2Flearn.microsoft.com%2Fen-us%2Fwindows%2Fwsl%2Fwsl-config


On Sat, Jul 29, 2023 at 6:27 AM Matthew Lynch  wrote:

>
> I was able to get recon-all-clinical working with 16 Gb computer.
>
> I thought the problem might be Windows hogging memory, so I created a live
> persistent USB install of lubuntu, using lubuntu 22 as a low resource
> distro in order to minimize memory usage, and installed freesurfer 7.4.0.
> Even with initial memory usage on 1Gb on lubuntu, synthseg still failed
> with out of memory error with 8 Gb swap file.  I watched the swap memory
> fill up and then process was killed.
>
> I added 16Gb swap using the following instructions, for a total swap space
> of 24 Gb + 16 Gb memory:
>
> https://secure-web.cisco.com/1ATUFZLp99G3zWsjWUI2HJaukRqMFcIimcs9TpbaIY-04Afcv6AnAqhXtv_tgDukEBDaKwCk0vi98Yo_CGHy_K0ixuTpGpvNyTNrWtDzAn3HiIrwLCM0XRljKu-f0ZBRxrw6K2OD_pOvEiIQtQD3oWtGq6wYRyF-4IBg22YWXBPz8JFai2hLSUOT0905dDFEps0_6H-G9XMI2XWSouiBCiL6-EkfX5ep2GT4dJKuI3x4U4yWDynhWh-LHvyQ4yqlzSO8lpYOVJyF4LdbcOLYGjP2u3NwKvCObnw3m3o59ENYo-LjZX3jSA241KQ_KYXiyiwemGYB_YOXHMZ0rBN_e_g/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-space
>
> This worked.
>
>
>
>
>
> On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch 
> wrote:
>
>> I do not have access to a computer with more RAM.  I can run recon-all
>> with 1mm T1 images without any problems.  How much RAM would
>> recon-all-clinical be expected to need?  Does it require less RAM if it
>> uses the GPU instead of CPU?
>>
>> On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <
>> bfis...@mgh.harvard.edu> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Can you try it on a computer with more ram?
>>>
>>>
>>>
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Matthew Lynch
>>> *Sent:* Thursday, July 13, 2023 1:55 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> *Subject:* [Freesurfer] recon-all-clinical out of memory error
>>>
>>>
>>>
>>> *External Email - Use Caution*
>>>
>>> I am having trouble running the new recon-all-clinical module.  I input
>>> 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be
>>> an out of memory error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu
>>> 22 on a computer with 16 Gb RAM.   Can anyone provide any thoughts on how
>>> to correct this?  Thanks in advance!
>>>
>>>
>>>
>>>  Here is the command:
>>>
>>>
>>>
>>> recon-all-clinical.sh ./T1AX5MM/119 fsclin 1
>>>
>>>
>>>
>>>
>>>
>>> here is the error output:
>>>
>>>
>>>
>>> SynthSeg-robust 2.0
>>> using CPU, hiding all CUDA_VISIBLE_DEVICES
>>> using 1 thread
>>> predicting 1/1
>>>
>>> the following problem occured with image
>>> /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :
>>> Traceback (most recent call last):
>>>   File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
>>> 315, in predict
>>> post_patch_segmentation, post_patch_parcellation, qc_score =
>>> net.predict([image, shape_input])
>>>   File
>>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
>>> line 70, in error_handler
>>> raise e.with_traceback(filtered_tb) from None
>>>   File
>>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py",
>>> line 52, in quick_execute
>>> tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name,
>>> op_name,
>>> tensorflow.python.framework.error

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

I was able to get recon-all-clinical working with 16 Gb computer.

I thought the problem might be Windows hogging memory, so I created a live
persistent USB install of lubuntu, using lubuntu 22 as a low resource
distro in order to minimize memory usage, and installed freesurfer 7.4.0.
Even with initial memory usage on 1Gb on lubuntu, synthseg still failed
with out of memory error with 8 Gb swap file.  I watched the swap memory
fill up and then process was killed.

I added 16Gb swap using the following instructions, for a total swap space
of 24 Gb + 16 Gb memory:

https://secure-web.cisco.com/1iFbhXQHpEFIJXXJqO_gzEOq97K25g0DNoKMVRh6pXcfEcG45FjIHKXyZ-aP4IALU-nPOQLDiOSqu0cFmHUgQutpHNu0uDVykcyNMml-zVextcU0zdKZS40VUf8z_9D7dIRdwaA3dnuN6rKOop5o_IBd0Xhm4gQmczEdE5SepDZMz9a0BGgeAbf09f3ZzPyuMDZXLwyERiQRVQPyJMHuGClyrhtUC7d4NJuP_9KRBoqeR9BA4fwwkEHxZ3pS9vdU4gongLDl_1Q8VBZYKrm2q6TtMZRzrvRcidoPwmB4YdcPTSMGaOV0N2NodjXNNXXpmYqkMsO42oxmBpIBrh1lWHA/https%3A%2F%2Faskubuntu.com%2Fquestions%2F178712%2Fhow-to-increase-swap-space

This worked.





On Thu, Jul 13, 2023 at 3:28 PM Matthew Lynch  wrote:

> I do not have access to a computer with more RAM.  I can run recon-all
> with 1mm T1 images without any problems.  How much RAM would
> recon-all-clinical be expected to need?  Does it require less RAM if it
> uses the GPU instead of CPU?
>
> On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <
> bfis...@mgh.harvard.edu> wrote:
>
>> External Email - Use Caution
>>
>> Can you try it on a computer with more ram?
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Matthew Lynch
>> *Sent:* Thursday, July 13, 2023 1:55 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] recon-all-clinical out of memory error
>>
>>
>>
>> *External Email - Use Caution*
>>
>> I am having trouble running the new recon-all-clinical module.  I input
>> 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be
>> an out of memory error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu
>> 22 on a computer with 16 Gb RAM.   Can anyone provide any thoughts on how
>> to correct this?  Thanks in advance!
>>
>>
>>
>>  Here is the command:
>>
>>
>>
>> recon-all-clinical.sh ./T1AX5MM/119 fsclin 1
>>
>>
>>
>>
>>
>> here is the error output:
>>
>>
>>
>> SynthSeg-robust 2.0
>> using CPU, hiding all CUDA_VISIBLE_DEVICES
>> using 1 thread
>> predicting 1/1
>>
>> the following problem occured with image
>> /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :
>> Traceback (most recent call last):
>>   File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
>> 315, in predict
>> post_patch_segmentation, post_patch_parcellation, qc_score =
>> net.predict([image, shape_input])
>>   File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
>> line 70, in error_handler
>> raise e.with_traceback(filtered_tb) from None
>>   File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py",
>> line 52, in quick_execute
>> tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name,
>> tensorflow.python.framework.errors_impl.ResourceExhaustedError: Graph
>> execution error:
>>
>> Detected at node 'model_5/unet_parc_merge_8/concat' defined at (most
>> recent call last):
>> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
>> 2642, in 
>>   main()
>> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
>> 162, in main
>>   predict(
>> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
>> 315, in predict
>>   post_patch_segmentation, post_patch_parcellation, qc_score =
>> net.predict([image, shape_input])
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
>> line 65, in error_handler
>>   return fn(*args, **kwargs)
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
>> line 2382, in predict
>>   tmp_batch_outputs = self.predict_function(iterator)
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
>> line 2169, in predict_function
>>   return step_function(self, iterator)
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
>> line 2155, in step_function
>>   outputs = model.distribute_strategy.run(run_step, args=(data,))
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
>> line 2143, in run_step
>>   outputs = model.predict_step(data)
>> File
>> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
>> line 2111, in predict_step
>>   return self(x, training=False)
>> File

Re: [Freesurfer] recon-all-clinical out of memory error

[Matthew Lynch]

External Email - Use Caution

I do not have access to a computer with more RAM.  I can run recon-all with
1mm T1 images without any problems.  How much RAM would recon-all-clinical
be expected to need?  Does it require less RAM if it uses the GPU instead
of CPU?

On Thu, Jul 13, 2023 at 1:58 PM Fischl, Bruce R.,PHD <
bfis...@mgh.harvard.edu> wrote:

> External Email - Use Caution
>
> Can you try it on a computer with more ram?
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Matthew Lynch
> *Sent:* Thursday, July 13, 2023 1:55 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] recon-all-clinical out of memory error
>
>
>
> *External Email - Use Caution*
>
> I am having trouble running the new recon-all-clinical module.  I input
> 5mm T1 axial DICOM images and it fails in SynthSeg with what appears to be
> an out of memory error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu
> 22 on a computer with 16 Gb RAM.   Can anyone provide any thoughts on how
> to correct this?  Thanks in advance!
>
>
>
>  Here is the command:
>
>
>
> recon-all-clinical.sh ./T1AX5MM/119 fsclin 1
>
>
>
>
>
> here is the error output:
>
>
>
> SynthSeg-robust 2.0
> using CPU, hiding all CUDA_VISIBLE_DEVICES
> using 1 thread
> predicting 1/1
>
> the following problem occured with image
> /mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
> 315, in predict
> post_patch_segmentation, post_patch_parcellation, qc_score =
> net.predict([image, shape_input])
>   File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
> line 70, in error_handler
> raise e.with_traceback(filtered_tb) from None
>   File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py",
> line 52, in quick_execute
> tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name,
> tensorflow.python.framework.errors_impl.ResourceExhaustedError: Graph
> execution error:
>
> Detected at node 'model_5/unet_parc_merge_8/concat' defined at (most
> recent call last):
> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
> 2642, in 
>   main()
> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
> 162, in main
>   predict(
> File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line
> 315, in predict
>   post_patch_segmentation, post_patch_parcellation, qc_score =
> net.predict([image, shape_input])
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
> line 65, in error_handler
>   return fn(*args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 2382, in predict
>   tmp_batch_outputs = self.predict_function(iterator)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 2169, in predict_function
>   return step_function(self, iterator)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 2155, in step_function
>   outputs = model.distribute_strategy.run(run_step, args=(data,))
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 2143, in run_step
>   outputs = model.predict_step(data)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 2111, in predict_step
>   return self(x, training=False)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
> line 65, in error_handler
>   return fn(*args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
> line 558, in __call__
>   return super().__call__(*args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
> line 65, in error_handler
>   return fn(*args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py",
> line 1145, in __call__
>   outputs = call_fn(inputs, *args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
> line 96, in error_handler
>   return fn(*args, **kwargs)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py",
> line 512, in call
>   return self._run_internal_graph(inputs, training=training, mask=mask)
> File
> "/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py",
> line 669, in _run_internal_g

Re: [Freesurfer] recon-all-clinical out of memory error

[Fischl, Bruce R.,PHD]

External Email - Use Caution

Can you try it on a computer with more ram?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Matthew Lynch
Sent: Thursday, July 13, 2023 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all-clinical out of memory error


External Email - Use Caution
I am having trouble running the new recon-all-clinical module.  I input 5mm T1 
axial DICOM images and it fails in SynthSeg with what appears to be an out of 
memory error.  I am running FreeSurfer 7.4.0 in WSL with Ubuntu 22 on a 
computer with 16 Gb RAM.   Can anyone provide any thoughts on how to correct 
this?  Thanks in advance!

 Here is the command:

recon-all-clinical.sh ./T1AX5MM/119 fsclin 1


here is the error output:

SynthSeg-robust 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 1 thread
predicting 1/1

the following problem occured with image 
/mnt/p/FreeSurfer/5MM/WM20120718/fsclin/mri/native.mgz :
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, in 
predict
post_patch_segmentation, post_patch_parcellation, qc_score = 
net.predict([image, shape_input])
  File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 70, in error_handler
raise e.with_traceback(filtered_tb) from None
  File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/tensorflow/python/eager/execute.py",
 line 52, in quick_execute
tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name,
tensorflow.python.framework.errors_impl.ResourceExhaustedError: Graph execution 
error:

Detected at node 'model_5/unet_parc_merge_8/concat' defined at (most recent 
call last):
File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 2642, 
in 
  main()
File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 162, 
in main
  predict(
File "/usr/local/freesurfer/7.4.0/python/scripts/mri_synthseg", line 315, 
in predict
  post_patch_segmentation, post_patch_parcellation, qc_score = 
net.predict([image, shape_input])
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 65, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 2382, in predict
  tmp_batch_outputs = self.predict_function(iterator)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 2169, in predict_function
  return step_function(self, iterator)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 2155, in step_function
  outputs = model.distribute_strategy.run(run_step, args=(data,))
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 2143, in run_step
  outputs = model.predict_step(data)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 2111, in predict_step
  return self(x, training=False)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 65, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/training.py",
 line 558, in __call__
  return super().__call__(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 65, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py",
 line 1145, in __call__
  outputs = call_fn(inputs, *args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 96, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py",
 line 512, in call
  return self._run_internal_graph(inputs, training=training, mask=mask)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/functional.py",
 line 669, in _run_internal_graph
  outputs = node.layer(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 65, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/engine/base_layer.py",
 line 1145, in __call__
  outputs = call_fn(inputs, *args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/keras/utils/traceback_utils.py",
 line 96, in error_handler
  return fn(*args, **kwargs)
File 
"/usr/local/freesurfer/7.4.0/python/lib/pytho

Re: [Freesurfer] recon-all ends with error

[Huang, Yujing]

External Email - Use Caution

It looks like you started recon-all by copying in mri/orig/001.mgz. I saw 
multiple runs of recon-all that were run on top of each other.

Can you try to restart clean by providing the input on the command line 
‘recon-all -s  -I  -all’?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Justin Kasowski
Sent: Wednesday, June 28, 2023 7:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all ends with error


External Email - Use Caution
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2023:06:28:16:19:10 mri_mask N 5 e 0.51 S 0.01 U 0.44 P 89% M 74240 
F 0 R 2972 W 0 c 3 w 760 I 0 O 0 L 0.13 0.04 0.01
@#@FSLOADPOST 2023:06:28:16:19:11 mri_mask N 5 0.13 0.04 0.01
#
#@# Fill Wed Jun 28 16:19:11 PDT 2023
/mnt/c/Users/BigBrain/documents/Subjects/sub-049/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta 
-segmentation aseg.presurf.mgz -ctab 
/usr/local/freesurfer/7.2.0/SubCorticalMassLUT.txt -auto-man filled.auto.mgz 
filled.mgz ../tmp/filled.edits.txt wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.presurf.mgz...
error: volume size must be greater than 0 in every dimension
Command exited with non-zero status 1

The error implies aseg.presurf.mgz or talairach.lta have a 0 dimension, but 
neither do. mri_info for aseg.presurf is below, I've attached the log and 
talairach.lta files:

bigbrain@DESKTOP-EDQPTKK:/mnt/c/Users/BigBrain/Documents/Subjects/sub-049/mri$ 
mri_info aseg.presurf.mgz
Volume information for aseg.presurf.mgz
  type: MGH
dimensions: 256 x 256 x 256
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Re: [Freesurfer] recon-all-clinical problems

[Michael Mc Laughlin]

External Email - Use Caution

So when I fixed those two _thresh errors in

https://secure-web.cisco.com/1NSg93ccyJ-d1nRYxQp22qqxh0VpV5ftKk_nXjpyVVwbCeR6Hrc55wa7clBot2_7TwVB60Mr2knHiVv8A4Mfl2qmBr5BYBGmlurvKxK7tkVb_5cRm_5FEI_GvOXQuD2koygzRKJ-i9xNxRvWZdKOxuYG-tyuRwO9v-AdgHd7Hh9JHtaZBxs_lSVtIP240zo9HyXSvshgmuVe4pfIrL4_Wvod_9PgcTNm9cAuaW-RaJK_zO9AOe8CixcXkaG_SLZQp9Ou86eoY5TJMOnUVWCBf_opB5Pl4QyOFRI0arqOWt-I6cur7E-SZu4pjFrkCzr3oJjVJhHsxQnclEt4462twOg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Frecon_all_clinical%2Frecon-all-clinical.sh

The script runs all the way through without any errors but there is still
one big problem and some smaller niggles:

1) The lateral ventricles are missing e.g. in mri/brain.mgz. I tried two
different T1 input images of the same brain.
2) The stats/aseg.stats file is missing
3) (Minor) It doesn't tell me how long it took to run which I found helpful
in the recon-all script


On Thu, Jun 22, 2023 at 4:30 PM Michael Mc Laughlin 
wrote:

> Actually, that is not the problem at all.
>
> I have found two errors in your script (the one on Github)
>
> There are two lines which refer to colortable_BA_thresh.txt that should
> say /colortable_BA.txt
>
> The script gets further when I fix those but I still have errors. The
> first one is:
>
> 
> Writing annot to
> /home/michael/subjects/jun23mpsynfix/label/rh.BA_exvivo.thresh.annot
> INFO: using TH3 volume calc
> INFO: assuming MGZ format for volumes.
> computing statistics for each annotation in ./rh.BA_exvivo.annot.
> reading volume /home/michael/subjects/jun23mpsynfix/mri/wm.mgz...
> reading input surface /home/michael/subjects/jun23mpsynfix/surf/rh.white...
> Using TH3 vertex volume calc
> Total face volume 254138
> Total vertex volume 253934 (mask=0)
> reading input pial surface
> /home/michael/subjects/jun23mpsynfix/surf/rh.pial...
> reading input white surface
> /home/michael/subjects/jun23mpsynfix/surf/rh.white...
> error: No such file or directory
> error: could not read annot file ./rh.BA_exvivo.annot
> ^^
> I think the first line here is writing to the wrong filename.
>
>
>
> On Thu, Jun 22, 2023 at 1:22 PM Michael Mc Laughlin 
> wrote:
>
>>
>> I found the problem. Your script has the following lines :
>>
>> You need to delete the fsaverage from the $SUBJECTS_DIR definition
>> because the lines following it put it in also.
>>
>> ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
>> cd ../label
>> # labels
>> set cmd="mri_label2label --srcsubject fsaverage --srclabel 
>> $SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.label
>> --trgsubject $SNAME --trglabel ./lh.BA1_exvivo.label --hemi lh
>> --regmethod surface"
>>
>>
>>
>> On Thu, Jun 22, 2023 at 11:23 AM Michael Mc Laughlin <
>> mich...@thecurate.com> wrote:
>>
>>> I tried recon-all-clinical and there are two main problems
>>>
>>> 1)  I ran it on a T1-MPRAGE image and it looks fine except that there
>>> are no lateral ventricles in the output. See attached.
>>>
>>> 2) I get lots of errors at the end.
>>>
>>> I read the following note in the release notes:
>>>
>>> *Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the
>>> latest version HERE
>>> .
>>> Development versions newer than June 15th 2023 do not have this problem.]*
>>>
>>> I am not a linux expert, so I don't know how to download that file. If I
>>> could download it I am sure I could manage to replace it in the bin
>>> directory.
>>>
>>> I made an attempt by clicking on the link and copying the text from my
>>> browser into a new text file. I used this to replace the supplied file, but
>>> I still get errors. Maybe I screwed up.
>>>
>>> Michael McLaughlin,
>>> Island View, Beulah Court,
>>> Harbour Road, Dalkey
>>> Co. Dublin
>>> Ph:+353 87 688 2514
>>>
>>>
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Re: [Freesurfer] recon-all-clinical problems

[Michael Mc Laughlin]

External Email - Use Caution

Actually, that is not the problem at all.

I have found two errors in your script (the one on Github)

There are two lines which refer to colortable_BA_thresh.txt that should say
/colortable_BA.txt

The script gets further when I fix those but I still have errors. The first
one is:


Writing annot to
/home/michael/subjects/jun23mpsynfix/label/rh.BA_exvivo.thresh.annot
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /home/michael/subjects/jun23mpsynfix/mri/wm.mgz...
reading input surface /home/michael/subjects/jun23mpsynfix/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 254138
Total vertex volume 253934 (mask=0)
reading input pial surface
/home/michael/subjects/jun23mpsynfix/surf/rh.pial...
reading input white surface
/home/michael/subjects/jun23mpsynfix/surf/rh.white...
error: No such file or directory
error: could not read annot file ./rh.BA_exvivo.annot
^^
I think the first line here is writing to the wrong filename.



On Thu, Jun 22, 2023 at 1:22 PM Michael Mc Laughlin 
wrote:

>
> I found the problem. Your script has the following lines :
>
> You need to delete the fsaverage from the $SUBJECTS_DIR definition because
> the lines following it put it in also.
>
> ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
> cd ../label
> # labels
> set cmd="mri_label2label --srcsubject fsaverage --srclabel 
> $SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.label
> --trgsubject $SNAME --trglabel ./lh.BA1_exvivo.label --hemi lh
> --regmethod surface"
>
>
>
> On Thu, Jun 22, 2023 at 11:23 AM Michael Mc Laughlin <
> mich...@thecurate.com> wrote:
>
>> I tried recon-all-clinical and there are two main problems
>>
>> 1)  I ran it on a T1-MPRAGE image and it looks fine except that there are
>> no lateral ventricles in the output. See attached.
>>
>> 2) I get lots of errors at the end.
>>
>> I read the following note in the release notes:
>>
>> *Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the
>> latest version HERE
>> .
>> Development versions newer than June 15th 2023 do not have this problem.]*
>>
>> I am not a linux expert, so I don't know how to download that file. If I
>> could download it I am sure I could manage to replace it in the bin
>> directory.
>>
>> I made an attempt by clicking on the link and copying the text from my
>> browser into a new text file. I used this to replace the supplied file, but
>> I still get errors. Maybe I screwed up.
>>
>> Michael McLaughlin,
>> Island View, Beulah Court,
>> Harbour Road, Dalkey
>> Co. Dublin
>> Ph:+353 87 688 2514
>>
>>
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Re: [Freesurfer] recon-all-clinical problems

[Michael Mc Laughlin]

External Email - Use Caution

I found the problem. Your script has the following lines :

You need to delete the fsaverage from the $SUBJECTS_DIR definition because
the lines following it put it in also.

ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
cd ../label
# labels
set cmd="mri_label2label --srcsubject fsaverage --srclabel
$SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.label
--trgsubject $SNAME --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod
surface"



On Thu, Jun 22, 2023 at 11:23 AM Michael Mc Laughlin 
wrote:

> I tried recon-all-clinical and there are two main problems
>
> 1)  I ran it on a T1-MPRAGE image and it looks fine except that there are
> no lateral ventricles in the output. See attached.
>
> 2) I get lots of errors at the end.
>
> I read the following note in the release notes:
>
> *Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest
> version HERE
> .
> Development versions newer than June 15th 2023 do not have this problem.]*
>
> I am not a linux expert, so I don't know how to download that file. If I
> could download it I am sure I could manage to replace it in the bin
> directory.
>
> I made an attempt by clicking on the link and copying the text from my
> browser into a new text file. I used this to replace the supplied file, but
> I still get errors. Maybe I screwed up.
>
> Michael McLaughlin,
> Island View, Beulah Court,
> Harbour Road, Dalkey
> Co. Dublin
> Ph:+353 87 688 2514
>
>
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Re: [Freesurfer] recon-all-clinical

[Iglesias Gonzalez, Juan E.]

External Email - Use Caution

Uuummm I don’t think this would work, as a lot of our intermediate files (eg 
norm.mgz) are not comparable to their counterparts in the standard recon-all 
stream. Sorry!

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1R9UOepVdGkzRhS_JbSZ7bkBYP0OujnEdjEaN6GrFG8xXfSYD4kdXxV5RSS22Efrjae1iNxYRieIPx_TYVzRGrhKR7IazpuzMz4Ym84t7daDKT2lROIZG2Ix9Ai0MCDWZBnw16XZaiV9NWdiAJEcywTAurIVkUFYUAh3Khky2RB1R2o14oO0NzRlpuI44mZpcM2bAbkTFbsInupFmBGqsCS3RpDiM9pgiOl8BTnlZa4P9JEsI7qWo6gmVLlhag_YbwWjigMA54QiSxrmN-r_iDg/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Date: Tuesday, June 20, 2023 at 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu , Iglesias 
Gonzalez, Eugenio , Gopinath, Karthik 

Subject: Re: [Freesurfer] recon-all-clinical

External Email - Use Caution

On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:

External Email - Use Caution
Hello Freesurfer experts!

I am conducting a longitudinal GMV and CT analysis of mTBI participants who 
received an experimental single-dose pharmacological treatment. We collected GE 
Bravo (0.9mm isotropic) T1w data pre, immediately after (~ 4 days after 
intervention) and 1-month following the intervention.

I have been working with the recon-all longitudinal pipeline stream  (7.1.1) 
but have noticed pretty significant errors in terms of skull stripping and 
segmentation (participants are veterans with somewhat random lesion / atrophy 
patterns).

I have tested your new recon-all-clinical program (7.4.0) on some of my worst 
cases and it is performing remarkably well. I am doing some more digging into 
the various synth segmentation packages available in FS newest versions and was 
wondering what the best course of action would be for integrating 
recon-all-clinical or synthseg into a longitudinal workflow.

1.Could I use the recon-all-clinical outputs as the "cross" for later base and 
long template construction?
I don't know. Hopefully Eugenio/Karthik will weigh in

2. SynthSeg and SCLimbic seem to have very good test-retest reliability-- would 
it be feasible to use the independent segmentation extractions from those and 
bypass the longitudinal stream entirely (not saying I would want to but I am 
curious)?
sclimbic generates segs that are not in the long stream, so there is no long 
option. My experience with synthseg is that it is inferior to the long stream 
on long data


Any and all help here would be greatly appreciated, and I thank you very much 
for your time.


Warmest regards,
Andrew



---



Andrew D. Geoly, MS



Research Data Analyst 1



Brain Stimulation Lab



Department of Psychiatry and Behavioral Sciences



Stanford University School of Medicine







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Re: [Freesurfer] recon-all-clinical

[Douglas N. Greve]

   External Email - Use Caution



On 5/26/2023 5:39 PM, Andrew Dedinas Geoly wrote:


External Email - Use Caution

Hello Freesurfer experts!

I am conducting a longitudinal GMV and CT analysis of mTBI 
participants who received an experimental single-dose pharmacological 
treatment. We collected GE Bravo (0.9mm isotropic) T1w data pre, 
immediately after (~ 4 days after intervention) and 1-month following 
the intervention.


I have been working with the recon-all longitudinal pipeline stream  
(7.1.1) but have noticed pretty significant errors in terms of skull 
stripping and segmentation (participants are veterans with somewhat 
random lesion / atrophy patterns).


I have tested your new recon-all-clinical program (7.4.0) on some of 
my worst cases and it is performing remarkably well. I am doing some 
more digging into the various synth segmentation packages available in 
FS newest versions and was wondering what the best course of action 
would be for integrating recon-all-clinical or synthseg into a 
longitudinal workflow.


1.Could I use the recon-all-clinical outputs as the "cross" for later 
base and long template construction?

I don't know. Hopefully Eugenio/Karthik will weigh in
2. SynthSeg and SCLimbic seem to have very good test-retest 
reliability-- would it be feasible to use the independent segmentation 
extractions from those and bypass the longitudinal stream entirely 
(not saying I would want to but I am curious)?
sclimbic generates segs that are not in the long stream, so there is no 
long option. My experience with synthseg is that it is inferior to the 
long stream on long data


Any and all help here would be greatly appreciated, and I thank you 
very much for your time.



Warmest regards,
Andrew


---

Andrew D. Geoly, MS

Research Data Analyst 1

Brain Stimulation Lab

Department of Psychiatry and Behavioral Sciences

Stanford University School of Medicine



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Re: [Freesurfer] recon-all

[fsbuild]

External Email - Use Caution

I think your SUBJECTS_DIR environment variable is still set to the default 
spath to ubject data that is set by default in the 7.2.0 release.  It is 
not intended that you add your own subjects in the freesurfer distribution as 
those are examples (and you don’t have write permission there on purpose). I 
would try manually setting (override) SUBJECTS_DIR in your environment to point 
to a path that is not under /usr/local, e.g., in your home drectory.  The 
akira subject data needs to live under a path set in SUBJECTS_DIR where you 
have both read/write permission.
- R.

On May 17, 2023, at 16:27, Douglas N. Greve  
wrote:External Email - Use 
Cautioncan't read that. can you 
cut-and-paste into the email?On 5/17/2023 1:29 PM, mahmoodasdfzjy 
wrote:External Email - Use 
CautionSorryI have a problem 
when I want to recon-all my T1-MPRAGE data.I face with this probmlem that 
attached it.Can you help 
me?ارسال
 شده از دستگاه Galaxy من___
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Re: [Freesurfer] recon-all error: cannot find or read colortable_BARe: recon-all error: cannot find or read colortable_BA_thresh.txt_thresh.txt

[fsbuild]

External Email - Use Caution

We should have an update for this installed there soon.
- R.
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Re: [Freesurfer] recon-all for GM quantification

[Fischl, Bruce R.,PHD]

External Email - Use Caution

Hi Sofia

Unfortunately that doesn't really work as the most time-intensive steps are 
required. We are working on replacing some of these with deep-learning 
equivalents, but it will be some months before that is available.

Sorry
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nikolaidou, Sofia
Sent: Friday, May 12, 2023 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all for GM quantification


External Email - Use Caution
Good afternoon,

My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the 
DCC project. I am reaching out to ask for your advice on a FreeSurfer question.

I am using recon-all to try to quantify and compare GM volume and mean 
thickness among our subjects. In essence, I think I have all the necessary 
measurements in the outcome files titled aseg.stats and ?h.aparc.stats. Would 
you happen to know how I can customize the stream and reduce the processing 
time by taking out steps from the -all process? In other words, what would be 
the minimal set of steps that I have to run in order to acquire the above 
output files?


Thank you in advance!

Kindly,
Sofia


Sofia Nikolaidou | Clinical Research Coordinator
MGH/HST Martinos Center for Biomedical Imaging
149 13th St, Charlestown, MA 02129
Phone: 617-417-4463
snikolai...@mgh.harvard.edu
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Re: [Freesurfer] recon-all not parcellating

[Carlos Estévez Fraga]

External Email - Use CautionSure! I’ll run it and let you know.I’ve also contacted the support team from the cluster in case there is any issue with the scriptMany thanksBest regardsCarlos Enviado desde mi iPhoneEl 10 mar 2023, a la(s) 14:47, Huang, Yujing  escribió:







Hi Carlos,
 
I’m not sure what happened. There are no errors reported in recon-all.log. Can you try running it again without ‘-parallel’?

 
Best,
 
Yujing
 


From: Carlos Estévez Fraga  
Sent: Friday, March 10, 2023 7:39 AM
To: Freesurfer support list ; Huang, Yujing 
Subject: Re: [Freesurfer] recon-all not parcellating


 
External Email - Use Caution
Sorry just wanted to follow up on this as not sure the email was received

 


Many thanks 


 


Best regards 


 


Carlos

Enviado desde mi iPhone






El 9 mar 2023, a la(s) 17:32, Carlos Estévez Fraga <cefr...@alumni.unav.es> escribió:





Sure I am attaching the recon-all file. 

 


Below is the output I get in the mri/ folder


 


I have also tried running recon-all -autorecon1 -autorecon2 -autorecon3 and it stops at the same place. 


 


Many thanks,


 


Best regards, 


 


Carlos


 


 


 


 



antsdn.brain.mgz

aseg.auto.mgz

aseg.auto_noCCseg.label_intensities.txt

aseg.auto_noCCseg.mgz

aseg.presurf.mgz

brain.finalsurfs.mgz

brainmask.auto.mgz

brainmask.mgz

brain.mgz

ctrl_pts.mgz

mri_nu_correct.mni.log

mri_nu_correct.mni.log.bak

norm.mgz

nu.mgz

orig

orig.mgz

orig_nu.mgz

rawavg.mgz

segment.dat

T1.mgz

talairach.label_intensities.txt

talairach.log

talairach_with_skull.log

transforms

wm.asegedit.mgz

wm.mgz

wm.seg.mgz


 


 


 


 


El jue, 9 mar 2023 a las 17:04, Huang, Yujing (<yhuan...@mgh.harvard.edu>) escribió:





Hi Carlos,
 
Can you send recon-all.log as attachment? So, we can have a better understanding of what happened.
 
Best,
 
Yujing
 

From:
freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Carlos Estévez Fraga
Sent: Thursday, March 9, 2023 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all not parcellating

 
External Email - Use Caution

Dear Freesurfer team,

 


I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is  recon-all
 -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256)


 


I have run the script different times with different subjects and it just stops abruptly always in the same point, after WM segmentation, see below the recon-all-status.log for
 one subject (same in all of them, it stops after WM segmentation)


 


I tried it on my laptop and in my desktop computer and it works, but not in the cluster...


 


Any chance you know why this may be happening? 


 


Best regards, 


 


Carlos


 


#@# MotionCor Tue Mar  7 22:10:08 GMT 2023
#@# Talairach Tue Mar  7 22:10:18 GMT 2023
#@# Talairach Failure Detection Tue Mar  7 22:13:37 GMT 2023
#@# Nu Intensity Correction Tue Mar  7 22:13:37 GMT 2023
#@# Intensity Normalization Tue Mar  7 22:16:54 GMT 2023
#@# Skull Stripping Tue Mar  7 22:18:15 GMT 2023
#@# EM Registration Tue Mar  7 22:20:49 GMT 2023
#@# CA Normalize Tue Mar  7 22:22:45 GMT 2023
#@# CA Reg Tue Mar  7 22:23:44 GMT 2023
#@# SubCort Seg Tue Mar  7 23:07:13 GMT 2023
#@# CC Seg Wed Mar  8 00:00:24 GMT 2023
#@# Merge ASeg Wed Mar  8 00:03:01 GMT 2023
#@# Intensity Normalization2 Wed Mar  8 00:03:01 GMT 2023
#@# Mask BFS Wed Mar  8 00:04:47 GMT 2023
#@# WM Segmentation Wed Mar  8 00:04:48 GMT 2023
#@# Fill Wed Mar  8 00:07:28 GMT 2023


 


 

--







Dr Carlos Estevez-Fraga, MD, PhD
Senior Clinical Research Fellow
Department of Neurodegenerative Diseases
UCL Queen Square Institute of Neurology
London, UK
Mail: c.fr...@ucl.ac.uk
Phone: +44 7788 926 982











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Re: [Freesurfer] recon-all not parcellating

[Huang, Yujing]

Hi Carlos,

I’m not sure what happened. There are no errors reported in recon-all.log. Can 
you try running it again without ‘-parallel’?

Best,

Yujing

From: Carlos Estévez Fraga 
Sent: Friday, March 10, 2023 7:39 AM
To: Freesurfer support list ; Huang, Yujing 

Subject: Re: [Freesurfer] recon-all not parcellating


External Email - Use Caution
Sorry just wanted to follow up on this as not sure the email was received

Many thanks

Best regards

Carlos
Enviado desde mi iPhone


El 9 mar 2023, a la(s) 17:32, Carlos Estévez Fraga 
mailto:cefr...@alumni.unav.es>> escribió:
Sure I am attaching the recon-all file.

Below is the output I get in the mri/ folder

I have also tried running recon-all -autorecon1 -autorecon2 -autorecon3 and it 
stops at the same place.

Many thanks,

Best regards,

Carlos





antsdn.brain.mgz

aseg.auto.mgz

aseg.auto_noCCseg.label_intensities.txt

aseg.auto_noCCseg.mgz

aseg.presurf.mgz

brain.finalsurfs.mgz

brainmask.auto.mgz

brainmask.mgz

brain.mgz

ctrl_pts.mgz

mri_nu_correct.mni.log

mri_nu_correct.mni.log.bak

norm.mgz

nu.mgz

orig

orig.mgz

orig_nu.mgz

rawavg.mgz

segment.dat

T1.mgz

talairach.label_intensities.txt

talairach.log

talairach_with_skull.log

transforms

wm.asegedit.mgz

wm.mgz

wm.seg.mgz




El jue, 9 mar 2023 a las 17:04, Huang, Yujing 
(mailto:yhuan...@mgh.harvard.edu>>) escribió:
Hi Carlos,

Can you send recon-all.log as attachment? So, we can have a better 
understanding of what happened.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Carlos Estévez Fraga
Sent: Thursday, March 9, 2023 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all not parcellating


External Email - Use Caution
Dear Freesurfer team,

I am trying to run recon-all -all in the cluster but unfortunately I am unable 
to obtain the parcellated images (exact command is  recon-all -parallel -openmp 
$NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256)

I have run the script different times with different subjects and it just stops 
abruptly always in the same point, after WM segmentation, see below the 
recon-all-status.log for one subject (same in all of them, it stops after WM 
segmentation)

I tried it on my laptop and in my desktop computer and it works, but not in the 
cluster...

Any chance you know why this may be happening?

Best regards,

Carlos

#@# MotionCor Tue Mar  7 22:10:08 GMT 2023
#@# Talairach Tue Mar  7 22:10:18 GMT 2023
#@# Talairach Failure Detection Tue Mar  7 22:13:37 GMT 2023
#@# Nu Intensity Correction Tue Mar  7 22:13:37 GMT 2023
#@# Intensity Normalization Tue Mar  7 22:16:54 GMT 2023
#@# Skull Stripping Tue Mar  7 22:18:15 GMT 2023
#@# EM Registration Tue Mar  7 22:20:49 GMT 2023
#@# CA Normalize Tue Mar  7 22:22:45 GMT 2023
#@# CA Reg Tue Mar  7 22:23:44 GMT 2023
#@# SubCort Seg Tue Mar  7 23:07:13 GMT 2023
#@# CC Seg Wed Mar  8 00:00:24 GMT 2023
#@# Merge ASeg Wed Mar  8 00:03:01 GMT 2023
#@# Intensity Normalization2 Wed Mar  8 00:03:01 GMT 2023
#@# Mask BFS Wed Mar  8 00:04:47 GMT 2023
#@# WM Segmentation Wed Mar  8 00:04:48 GMT 2023
#@# Fill Wed Mar  8 00:07:28 GMT 2023


--
Dr Carlos Estevez-Fraga, MD, PhD
Senior Clinical Research Fellow
Department of Neurodegenerative Diseases
UCL Queen Square Institute of Neurology
London, UK
Mail: c.fr...@ucl.ac.uk<mailto:c.fr...@ucl.ac.uk>
Phone: +44 7788 926 982
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<https://www.massgener

Re: [Freesurfer] recon-all not parcellating

[Carlos Estévez Fraga]

External Email - Use CautionSorry just wanted to follow up on this as not sure the email was receivedMany thanks Best regards CarlosEnviado desde mi iPhoneEl 9 mar 2023, a la(s) 17:32, Carlos Estévez Fraga  escribió:Sure I am attaching the recon-all file. Below is the output I get in the mri/ folderI have also tried running recon-all -autorecon1 -autorecon2 -autorecon3 and it stops at the same place. Many thanks,Best regards, Carlos





antsdn.brain.mgz
aseg.auto.mgz
aseg.auto_noCCseg.label_intensities.txt
aseg.auto_noCCseg.mgz
aseg.presurf.mgz
brain.finalsurfs.mgz
brainmask.auto.mgz
brainmask.mgz
brain.mgz
ctrl_pts.mgz
mri_nu_correct.mni.log
mri_nu_correct.mni.log.bak
norm.mgz
nu.mgz
orig
orig.mgz
orig_nu.mgz
rawavg.mgz
segment.dat
T1.mgz
talairach.label_intensities.txt
talairach.log
talairach_with_skull.log
transforms
wm.asegedit.mgz
wm.mgz
wm.seg.mgzEl jue, 9 mar 2023 a las 17:04, Huang, Yujing () escribió:







Hi Carlos,
 
Can you send recon-all.log as attachment? So, we can have a better understanding of what happened.
 
Best,
 
Yujing
 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of Carlos Estévez Fraga
Sent: Thursday, March 9, 2023 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all not parcellating

 
External Email - Use Caution

Dear Freesurfer team,

 


I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is  recon-all
 -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256)


 


I have run the script different times with different subjects and it just stops abruptly always in the same point, after WM segmentation, see below the recon-all-status.log for one subject (same in all of them, it stops after WM segmentation)


 


I tried it on my laptop and in my desktop computer and it works, but not in the cluster...


 


Any chance you know why this may be happening? 


 


Best regards, 


 


Carlos


 


#@# MotionCor Tue Mar  7 22:10:08 GMT 2023
#@# Talairach Tue Mar  7 22:10:18 GMT 2023
#@# Talairach Failure Detection Tue Mar  7 22:13:37 GMT 2023
#@# Nu Intensity Correction Tue Mar  7 22:13:37 GMT 2023
#@# Intensity Normalization Tue Mar  7 22:16:54 GMT 2023
#@# Skull Stripping Tue Mar  7 22:18:15 GMT 2023
#@# EM Registration Tue Mar  7 22:20:49 GMT 2023
#@# CA Normalize Tue Mar  7 22:22:45 GMT 2023
#@# CA Reg Tue Mar  7 22:23:44 GMT 2023
#@# SubCort Seg Tue Mar  7 23:07:13 GMT 2023
#@# CC Seg Wed Mar  8 00:00:24 GMT 2023
#@# Merge ASeg Wed Mar  8 00:03:01 GMT 2023
#@# Intensity Normalization2 Wed Mar  8 00:03:01 GMT 2023
#@# Mask BFS Wed Mar  8 00:04:47 GMT 2023
#@# WM Segmentation Wed Mar  8 00:04:48 GMT 2023
#@# Fill Wed Mar  8 00:07:28 GMT 2023


 


 

-- 






Dr Carlos Estevez-Fraga, MD, PhD
Senior Clinical Research Fellow
Department of Neurodegenerative Diseases
UCL Queen Square Institute of Neurology
London, UK
Mail: c.fr...@ucl.ac.uk
Phone: +44 7788 926 982












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-- Dr Carlos Estevez-Fraga, MD, PhDSenior Clinical Research FellowDepartment of Neurodegenerative DiseasesUCL Queen Square Institute of NeurologyLondon, UKMail: c.fr...@ucl.ac.ukPhone: +44 7788 926 982
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Re: [Freesurfer] recon-all not parcellating

[Huang, Yujing]

Hi Carlos,

Can you send recon-all.log as attachment? So, we can have a better 
understanding of what happened.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Carlos Estévez Fraga
Sent: Thursday, March 9, 2023 9:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all not parcellating


External Email - Use Caution
Dear Freesurfer team,

I am trying to run recon-all -all in the cluster but unfortunately I am unable 
to obtain the parcellated images (exact command is  recon-all -parallel -openmp 
$NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256)

I have run the script different times with different subjects and it just stops 
abruptly always in the same point, after WM segmentation, see below the 
recon-all-status.log for one subject (same in all of them, it stops after WM 
segmentation)

I tried it on my laptop and in my desktop computer and it works, but not in the 
cluster...

Any chance you know why this may be happening?

Best regards,

Carlos

#@# MotionCor Tue Mar  7 22:10:08 GMT 2023
#@# Talairach Tue Mar  7 22:10:18 GMT 2023
#@# Talairach Failure Detection Tue Mar  7 22:13:37 GMT 2023
#@# Nu Intensity Correction Tue Mar  7 22:13:37 GMT 2023
#@# Intensity Normalization Tue Mar  7 22:16:54 GMT 2023
#@# Skull Stripping Tue Mar  7 22:18:15 GMT 2023
#@# EM Registration Tue Mar  7 22:20:49 GMT 2023
#@# CA Normalize Tue Mar  7 22:22:45 GMT 2023
#@# CA Reg Tue Mar  7 22:23:44 GMT 2023
#@# SubCort Seg Tue Mar  7 23:07:13 GMT 2023
#@# CC Seg Wed Mar  8 00:00:24 GMT 2023
#@# Merge ASeg Wed Mar  8 00:03:01 GMT 2023
#@# Intensity Normalization2 Wed Mar  8 00:03:01 GMT 2023
#@# Mask BFS Wed Mar  8 00:04:47 GMT 2023
#@# WM Segmentation Wed Mar  8 00:04:48 GMT 2023
#@# Fill Wed Mar  8 00:07:28 GMT 2023


--
Dr Carlos Estevez-Fraga, MD, PhD
Senior Clinical Research Fellow
Department of Neurodegenerative Diseases
UCL Queen Square Institute of Neurology
London, UK
Mail: c.fr...@ucl.ac.uk
Phone: +44 7788 926 982
___
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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] Recon-all exited without errors

[Douglas N. Greve]

That one looks like there was a massive failure of the registration. One 
thing you can try is to add -samseg-reg to the command line. This will 
use samseg to do this registration, which may be more robust. Is there 
anything amiss with your image?


On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:


External Email - Use Caution

Thanks for the response.  I should have been more clear in my first 
email.  I have used tkregister2 in the past to fix talairachs, but 
this one does not appear to be fixable with the in-plane shifting, 
scaling, and rotating that is available within the tkregister2 GUI.  
The moveable appears to be in a different plane than the target. I’m 
attaching a screenshot from tkregister2.


Is there a different way to fix the talairach or another recon fix 
(especially considering the apparent brainmask issue) that should be 
pursued?


Thanks again for your help!

*Bryna Goeckner* (she/her)

Graduate Student

Meier Lab

Medical College of Wisconsin

Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:


Content-Type: text/plain; charset="us-ascii"

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the 
talairach registration:


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://urldefense.com/v3/__https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$ 
<https://secure-web.cisco.com/1HZhWFe_X3bRyu1YMrXe-GHFqQMAp04dAp8aVbI-P4-kd9XuX7fVsWdo1N2FV-BK7Kbf14_mEbYcXBej0M7TxUI7FxJQn3tng1J51U4hRi6nWKqOVDjTQW9jAl1K5WpUp9DHONveLfGOggQk-eQOGTf6wFZcvs9mW9PKB5ewCbuL7PDrj1TZ_8uLc1Tok2eS4q24SZBfZcAiNNTjfLW1EdnIaPouA3ruo1ZSk0hOUYTMzcKamBpdVrUjcMHmI6SQEMhGj7_9lxwuB28WuR_Q_IFQLF6vFx7W_lnh8vtBlI0akxRMt_YFuxDJVCWcJvxPW4ohMXUYGOWgJznRPRJrH7w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__%3B%21%21H8mHWRdzp34%21_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY%24>


Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna

Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


    External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with 
errors (looks like for talairach issues) but I am not able to use 
tkregister2 to view and make manual adjustments to the talairach since 
surf/lh.orig was not generated.


I then tried recon-all with the -notal-check flag, which exited 
"without errors" although the talairach is nowhere near correctly 
aligned and while aparc & aseg in freeview appear ok, the brainmask 
appears to have issues (when I turn it off, the entire background 
displays as white).


I'm including the recon-all logs (original & notal-check flag) and 
have listed the actual commands used below as well.  Any help you can 
provide in figuring out how to run this subject is greatly 
appreciated.  Thanks!


The original code was:
recon-all -subject subj# \
    -i rawT1.nii.gz \
    -T2 rawT2.nii.gz \
    -T2pial \
    -parallel -openmp 12 \
    -3T \
    -all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program


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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] recon-all does not produce ?h.white files

[Huang, Yujing]

You can find information about recon-all process here 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Add '-finalsurfs' to you recon-all command line options.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Faraz 
Yazdanibanafshedaragh
Sent: Wednesday, February 15, 2023 3:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all does not produce ?h.white files


External Email - Use Caution
Hello,

When I use the command recon-all  -autorecon2-wm -subjid ${tmp_subj} -noaseg 
-xopts-use I only get ?h.white.K and ?h.white.H files, but not the ?h.white 
file that I need for mri_vol2surf script (so it exits with error). What am I 
doing wrong?

Thank you
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Re: [Freesurfer] Recon-all exited without errors

[Goeckner, Bryna]

External Email - Use Caution

Thanks for the response.  I should have been more clear in my first email.  I 
have used tkregister2 in the past to fix talairachs, but this one does not 
appear to be fixable with the in-plane shifting, scaling, and rotating that is 
available within the tkregister2 GUI.  The moveable appears to be in a 
different plane than the target. I’m attaching a screenshot from tkregister2.

Is there a different way to fix the talairach or another recon fix (especially 
considering the apparent brainmask issue) that should be pursued?

Thanks again for your help!

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the talairach 
registration:

https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9YeKKqov5FFLfo7EJ1tkbdCb8krY7nQttKhgmNZCXK5L94ZpFhJkWTFUHHIAx2IOPV6NdbjrrR8l5to2eYyjf7f73q0gxzvGRqPjFYJSbx6RnU2e6Y0Y845X5iZK0gJjKf0ocZfzbtnDxSQPa9rAacjR4rEiApsikJTcm8bqKneABuY85pIGXSVGaAlmOYhwc2jnJOim5ip-CHBIWC6YBOUNw73onOe9612EeLkDlFEN7mTxvA6ddcLM4B5FXXvr0imuo4Q0yko_o4jFQXiRG_YNEBEk4HApUCE4KmVHr2w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREnWme11f5wwS_mX9Rx4UP523Br2Cnzb57bqvcJ2PLBpiR5k410ksn7Q23xaG_tnK045KUyPlp2rv7s6Kq2pte4t73E-NqHvoLJFuWAySX2iOqlRGRmOaLPmHkm5Vk9y5Jj5SO3Ndt8nUQS657skk6jrPN5DJXr8S4FayfpfrGAxz9djtI9_5v63yyeGK9B7IHShMLkrd7mOgTgg91nQQ8j57F_1qykXxnrxZ1SEHy714L5pyC2GzySNFbxWd0_mqGSYYIxDNNLByDVDIEeNVktgup-0CUh10JQIsW5HhPUQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$>

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with errors 
(looks like for talairach issues) but I am not able to use tkregister2 to view 
and make manual adjustments to the talairach since surf/lh.orig was not 
generated.

I then tried recon-all with the -notal-check flag, which exited "without 
errors" although the talairach is nowhere near correctly aligned and while 
aparc & aseg in freeview appear ok, the brainmask appears to have issues (when 
I turn it off, the entire background displays as white).

I'm including the recon-all logs (original & notal-check flag) and have listed 
the actual commands used below as well.  Any help you can provide in figuring 
out how to run this subject is greatly appreciated.  Thanks!

The original code was:
recon-all -subject subj# \
-i rawT1.nii.gz \
-T2 rawT2.nii.gz \
-T2pial \
-parallel -openmp 12 \
-3T \
-all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
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Re: [Freesurfer] Recon-all exited with errors

[Huang, Yujing]

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the talairach 
registration:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with errors 
(looks like for talairach issues) but I am not able to use tkregister2 to view 
and make manual adjustments to the talairach since surf/lh.orig was not 
generated.

I then tried recon-all with the -notal-check flag, which exited "without 
errors" although the talairach is nowhere near correctly aligned and while 
aparc & aseg in freeview appear ok, the brainmask appears to have issues (when 
I turn it off, the entire background displays as white).

I'm including the recon-all logs (original & notal-check flag) and have listed 
the actual commands used below as well.  Any help you can provide in figuring 
out how to run this subject is greatly appreciated.  Thanks!

The original code was:
recon-all -subject subj# \
-i rawT1.nii.gz \
-T2 rawT2.nii.gz \
-T2pial \
-parallel -openmp 12 \
-3T \
-all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier 
Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
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Re: [Freesurfer] recon-all terminates with error

[Huang, Yujing]

The problem is in your dicom files. They are missing Image Orientation 
(0020,0037) attribute, which specifies the direction cosines of the first row 
and the first column with respect to the patient. I believe you need to check 
how the image was scanned/saved at the scanner.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of MANSON ERIC NAAB
Sent: Friday, January 6, 2023 12:37 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all terminates with error


External Email - Use Caution
Thank you for your quick response. Please,  can you kindly assist me with 
freesurfer input image template for sT1-weighted? How do I solve this 
orientation problem?

Thank you.

On Fri, 6 Jan 2023, 14:34 Huang, Yujing, 
mailto:yhuan...@mgh.harvard.edu>> wrote:
It looks like there is a problem with your input dicom file - image orientation 
tag is missing.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of MANSON ERIC NAAB
Sent: Thursday, January 5, 2023 11:15 PM
To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all terminates with error


External Email - Use Caution
Dear FreeSurfer experts,
I am a first time  FreeSurfer user trying to run a recon-all for a sT1_W image. 
However, recon-all terminates with an error "tag image orientation not found" I 
need help on how to resolve this.

Kindly find the recon-all.log file.
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Re: [Freesurfer] recon-all terminates with error

[MANSON ERIC NAAB]

External Email - Use Caution

Thank you for your quick response. Please,  can you kindly assist me with
freesurfer input image template for sT1-weighted? How do I solve this
orientation problem?

Thank you.

On Fri, 6 Jan 2023, 14:34 Huang, Yujing,  wrote:

> It looks like there is a problem with your input dicom file - image
> orientation tag is missing.
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *MANSON ERIC NAAB
> *Sent:* Thursday, January 5, 2023 11:15 PM
> *To:* Freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] recon-all terminates with error
>
>
>
> *External Email - Use Caution*
>
> Dear FreeSurfer experts,
>
> I am a first time  FreeSurfer user trying to run a recon-all for a sT1_W
> image. However, recon-all terminates with an error "tag image orientation
> not found" I need help on how to resolve this.
>
>
>
> Kindly find the recon-all.log file.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1cyshhNaiz2kv9367zAck0S2C8VINgCWouegtdexAFGectdcsXx-Mtc4RHf389neaMtixuld6aFZJbTRR_Cr0OHMpMSCVgtb3zYIk4fpKCG2wpps7BCEmJD88pyv4fstNWk4SCjlZ7tp01Mgz5Dhxbib52ajsoIIExXbya0blRlQq7EgICzC_vnHrC4MWYwAFlshgoJNM0bvMvgo1JsWq1ePg_zGR6wg_zY_25lMznOrEnSZOAbeXHEJeAVFsX8xxsUjhuO-TXCsZrvaQfaYLFdXJjKC9hFGg6j0vBZg5dy9wmvpADeMThgGuEhUVUZwmlZv58GvUOxcy85Lr36vTb_8GEGQkJPN9B9q_cNGv6fc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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>  <
> https://secure-web.cisco.com/1R_7R1drwnmipruEFp9CeuohI96c58n_wwMNhxtj8NrvwpTYhG5znRFUd5FseDSfwh4KiHlvh5s2sJr7hXQAhrfA8h6_XqcD8khKN0gbnkIo9WvVHsrg93Tuy554sCLWm-o-Tl9qzsIdz7ksgrxwo6AICckx7J7tqEE3gMBiZPDQGWuY-pCgi0JZVx_qJzikFsp3QJNxg035ThncbInuC-TcDWi3X3hjFTLtEHqeRKfrDqW9Q_TOrWj5WYDqTblZJ9XJuUgHI1siHrcMdw7Ukrb77stTx4y28c3fLZck8b_uWAFCUOAkkkJN-fCYorlJ-3w1JdgrtCMpoGYMQOLhXgkVAd20hdlwu5ehIcQWYPh8/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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Re: [Freesurfer] recon-all terminates with error

[Huang, Yujing]

It looks like there is a problem with your input dicom file - image orientation 
tag is missing.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of MANSON ERIC NAAB
Sent: Thursday, January 5, 2023 11:15 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all terminates with error


External Email - Use Caution
Dear FreeSurfer experts,
I am a first time  FreeSurfer user trying to run a recon-all for a sT1_W image. 
However, recon-all terminates with an error "tag image orientation not found" I 
need help on how to resolve this.

Kindly find the recon-all.log file.
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Re: [Freesurfer] recon-all failing to generate wm surface

[Huang, Yujing]

Hi Christopher,

I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I 
don't think ?h.white surface are generated for the command combinations. 
'recon-all -all' will run all recon steps and generate ?h.white.

Here is a description of recon-all process and flags:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Christopher Mcnorgan
Sent: Wednesday, November 23, 2022 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all failing to generate wm surface


External Email - Use Caution
A student and I have independently been trying to reconstruct a dataset. We've 
tried it a couple different ways using either an additional FLAIR or a T2 image 
and always hit a point where the process halts because of a missing surface 
file:

Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file

This has happened when running just the autorecon1 step or both autorecon1 and 
autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is 
running 7.3.2 on a Mac. In my most recent test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2  
-subjid 
and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but 
not the ?h.white surface. I'm unclear what's causing the recon-all script to 
look for the wm surface before it's been created.
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Re: [Freesurfer] recon-all failing to generate wm surface

[Douglas N. Greve]

please send the recon-all.log file

On 11/23/2022 5:10 PM, Christopher Mcnorgan wrote:


External Email - Use Caution

A student and I have independently been trying to reconstruct a 
dataset. We've tried it a couple different ways using either an 
additional FLAIR or a T2 image and always hit a point where the 
process halts because of a missing surface file:


Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not 
open file


This has happened when running just the autorecon1 step or both 
autorecon1 and autorecon2. I'm using freesurfer 7.2.0 on a linux 
computer, and my student is running 7.3.2 on a Mac. In my most recent 
test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2 file> -subjid 
and I have several surface files (e.g., ?h.orig and even 
?h.white.preaparc) but not the ?h.white surface. I'm unclear what's 
causing the recon-all script to look for the wm surface before it's 
been created.


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The information in this e-mail is intended only for the person to whom it is 
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all failing to generate wm surface

[Huang, Yujing]

Hi Christopher,

I noticed that you were only running 'recon-all -autorecon1 -autorecon2'. I 
don't think ?h.white surface are generated for the command combinations. 
'recon-all -all' will run all recon steps and generate ?h.white.

Here is a description of recon-all process and flags:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Christopher Mcnorgan
Sent: Wednesday, November 23, 2022 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all failing to generate wm surface


External Email - Use Caution
A student and I have independently been trying to reconstruct a dataset. We've 
tried it a couple different ways using either an additional FLAIR or a T2 image 
and always hit a point where the process halts because of a missing surface 
file:

Loading lh.white surf
error: No such file or directory
error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file

This has happened when running just the autorecon1 step or both autorecon1 and 
autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is 
running 7.3.2 on a Mac. In my most recent test, I ran
recon-all -autorecon1 -autorecon2 -i  -T2  
-subjid 
and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but 
not the ?h.white surface. I'm unclear what's causing the recon-all script to 
look for the wm surface before it's been created.
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contains patient information, please contact the Mass General Brigham 
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 .
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