Re: [Freesurfer] I cannot edit white matter mask

2022-01-27 Thread Rosalia Dacosta Aguayo 
External Email - Use Caution

Hi Douglas,

Thank you for your reply. I mean that the voxels do not change the color
value 255. Is like nothing is happening to them.

What do you mean by if the surfaces are not following the gray white
boundary. It is not used for anything else? If this is the case, should I
discard this subject?

Kind regards,
Rosie




On Fri, Jan 28, 2022 at 12:44 AM Douglas N. Greve 
wrote:

> If it works for others, then I don't know what could be going wrong. Also,
> it is unclear what you mean by not being able to edit it (permission?
> voxels don't change). Also note that you only need  to change the wm.mgz if
> the surfaces are not following the gray white boundary. It is not used for
> anything else.
>
> On 1/27/2022 8:41 AM, Rosalia Dacosta Aguayo wrote:
>
> External Email - Use Caution
> Dear Freesurfer team,
>
> I am quality-checking the segmentation work from FreeSurfer version 7.1
> and I have a  subject whose white matter mask I cannot edit. I wonder why
> is this happening?
>
> The white matter mask has a lot of holes and the brush does not work over
> them. I know the brush is working because I have been editing other white
> matter masks but this subject is different.
>
> Any help would be appreciated
>
> My best regards,
> Rosie
>
>
>
> ___
> Freesurfer mailing 
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>
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Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-27 Thread falk.luesebr...@med.ovgu.de 
External Email - Use Caution

Glad to hear it worked out in the end.


Best,

Falk


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Nathan Kindred (PGR) 

Gesendet: Donnerstag, 27. Januar 2022 12:20:52
An: Freesurfer support list
Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer


External Email - Use Caution
Hi both,

Thank you so much to both of you for the help. I have now managed to get it to 
work using Falk’s command. I’ve made a note of your suggestion too, Douglas, 
just in case I have any errors with other subjects.

Best,
Nathan

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

Date: Wednesday, 26 January 2022 at 21:52
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
I think that should work.
One other issue is that the wm.seg.mgz might need to be uchar (a relic
of when computers did not have so much memory). If it does not work with
falk's command, you can try
mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz


On 1/24/2022 2:47 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Oh, sorry... Following the steps from the previous mail you should run this 
> command:
>
>
> mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz
>
>
> Best,
>
> Falk
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von 
> falk.luesebr...@med.ovgu.de 
> Gesendet: Montag, 24. Januar 2022 08:41:15
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
>
>  External Email - Use Caution
>
> Hi Nathan,
>
>
> well, once again, I can't be much of help with regards to your error message. 
> Have you had a look at the data and does it looks reasonable up to that 
> point? Which FreeSurfer version are you running?
>
>
> FreeSurfer needs to have the data in a very specific form. In case of the 
> white matter segmentation the resulting volume should have a value of 110 
> where white matter is located. The SPM segmentation has values of 0 to 1. 
> Therefore, if you would simply try to use that, it wouldn't work. The given 
> command should do that while using the SPM segmentation to mask the 
> brain.mgz. Afterwards, the ventricles and subcortical structures will be 
> filled based on the aseg.presurf.mgz and set to values of 250. The other 
> commands changes the WM segmentation so that the neighbors of all voxels 
> labeled as WM have a face in common - no edges or corners allowed.
>
>
> Best,
>
> Falk
>
>
>  "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/14nwA-wqvm5kUO9O0CsIsE56npxQFbhl00lDoBBn2Lt0jPyQd2MOLdD6qyI7YDiLjFj2iBWdyjbc3GFnQRYrJbJEGplbV7Yi75yeodKQxt6wQXGAJJFATFWE7Cup4jEtDmDUaIXp2MFMQm9jbSWGlNTCdHAYSaU60VTRi3UToEmalYfSvSd3LkEPhCRvXlCfOqGDCkBbs-KXI7dRab7n15-VsUqDVncyW5pIk-OBdL7twQx1TD-FOf8cRs6UROEuM5RpQFZgc-vR_hyQHMLpbvPJDiNN7DqErbTiXKnVg6P7fkHfVJnFA3rzcFdOe3yMAFl9AUZ9ndlL-2kWb1T1wPQ/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsecure-web.cisco.com%252F1mIUaa7F-i8b4cYwNnbztpMSGC1LS0vhF8ATfmhtgiZxT6lh0vSh_fcPYFd0tYgHhhlC0czxOdn69ctn9ZyRSKCYMcXsmmkriPcmLaomDWhtmJ5W4il1ZwhsIARbrSX2L7lwOY4WpeD17uvDPZEr9lJH-8xglQ5ObufKxfy2D3vtvwE2N-M8VOR-hEb0TVWvq5U9gQ4kxRHAcpk8alzRctnBGXIBmyM_-d1Aj1RjAD6VdhMQjTTWweZbJ9MvFjIDFEoeAmvs02ErbmlqFjhY8W97SzZV2Z2hoWaCtKNzqWxvGDQld_eKtmrykF9fMby4w%252Fhttp%25253A%25252F%25252Fwww.kneu.ovgu.de%25252Fkneu.html%26data%3D04%257C01%257Cn.kindred1%2540newcastle.ac.uk%257Ce41576f561da483306eb08d9e116165f%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C637788307247196211%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D0ejbAPnogyKL0%252FkmGEBUrBLIWh9a%252F%252Bd%252FGtlAzVEfKJY%253D%26reserved%3D0

Re: [Freesurfer] Problems with recon for manually fixed

2022-01-27 Thread Douglas N. Greve 
Can you send the recon-all.log?

On 1/27/2022 9:34 AM, Goeckner, Bryna wrote:
>  External Email - Use Caution
>
> We are using FS 7.2
>
> Bryna Goeckner (she/her)
> Graduate Student
> Medical College of Wisconsin
> Neuroscience Doctoral Program
>
> Date: Wed, 26 Jan 2022 16:43:44 -0500
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] Problems with recon for manually fixed
>  Talairach
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <8e0752c5-13fa-755e-c416-4253ce504...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> what version of FS are you using?
>
> On 1/21/2022 2:21 PM, Goeckner, Bryna wrote:
>> External Email - Use Caution
>>
>> Hi,
>>
>> I am trying to decide how to proceed after manually updating a
>> talairach since various ways I?ve tried the recon process give me
>> different results.
>>
>> Our group used Freesurfer 7.2 for processing data with the T2 and 3T
>> flags as follows:
>>
>> recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 $2/rawT2.ORIG.nii.gz
>> -T2pial -parallel -openmp 12 -3T -all
>>
>> After visual inspection, I made adjustments to the talairach using
>> tkregister2 and then used the code below to rerun the recon:
>>
>> recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel
>> -openmp 12 -3T? -all
>>
>> When this was done, the talairach.xfm file was restored to the
>> talairach from the original recon, while the talairach.xfm~ was still
>> the fixed version. At no point in this entire process did the
>> talairach (fixed or original) generate an error.
>>
>> To avoid the overwriting of the talairach.xfm file, I tried using
>> (separately) the -notalairach and -notal-check flags. For both, the
>> talairach.xfm file stayed as the fixed talairach, but I got different
>> aseg and aparc results.
>>
>> I?d like to know more about how these to flags differ and if you have
>> a recommendation on which process is best.? The plan is to eventually
>> use this data in TRACULA.
>>
>> Thanks for your help,
>>
>> *Bryna Goeckner*?(she/her)
>>
>> Graduate Student
>>
>> Medical College of Wisconsin
>>
>> Neuroscience Doctoral Program
>
>
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Re: [Freesurfer] I cannot edit white matter mask

2022-01-27 Thread Douglas N. Greve 
If it works for others, then I don't know what could be going wrong. 
Also, it is unclear what you mean by not being able to edit it 
(permission? voxels don't change). Also note that you only need  to 
change the wm.mgz if the surfaces are not following the gray white 
boundary. It is not used for anything else.


On 1/27/2022 8:41 AM, Rosalia Dacosta Aguayo wrote:


External Email - Use Caution

Dear Freesurfer team,

I am quality-checking the segmentation work from FreeSurfer version 
7.1 and I have a  subject whose white matter mask I cannot edit. I 
wonder why is this happening?


The white matter mask has a lot of holes and the brush does not work 
over them. I know the brush is working because I have been editing 
other white matter masks but this subject is different.


Any help would be appreciated

My best regards,
Rosie

*
*


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Re: [Freesurfer] The better way to turn off PVC?

2022-01-27 Thread Douglas N. Greve 
You need to use both to totally turn it off. There are two types of 
PVEs. One is due to blurring/smoothing (fixed with --psf). The other is 
due to multiple tissue types being in the same voxel (the tissue 
fraction effect (TFE))



On 1/27/2022 12:40 PM, Zhener Zhang wrote:


External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command:

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg 
gtmseg.mgz

--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off:

One is to set the point-spread function to 0 by adding “—psf 0”,
The other one is to get rid of “—psf” altogether and add “—no-tfe”.

We tried both and they produced slightly different results. The second 
method “—no-tfe” produced lower uptake values for each ROI. Which one 
would you recommend to properly turn PVC off? Thanks in advance!


Best regards,
Zhener

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[Freesurfer] The better way to turn off PVC?

2022-01-27 Thread Zhener Zhang 
External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command:

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off:
One is to set the point-spread function to 0 by adding “—psf 0”,
The other one is to get rid of “—psf” altogether and add “—no-tfe”.

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance!

Best regards,
Zhener
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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

2022-01-27 Thread Zhener Zhang 
External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

2022-01-27 Thread Zhener Zhang 
External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

2022-01-27 Thread Zhener Zhang 
External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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Re: [Freesurfer] Error in mri_glmfit

2022-01-27 Thread Laura Willers de Souza 
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Sorry for such a simple mistake and thank you so much for all the help!

Best,
Laura.
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Re: [Freesurfer] Using SPM segmentations in FreeSurfer

2022-01-27 Thread Nathan Kindred (PGR) 
External Email - Use Caution

Hi both,

Thank you so much to both of you for the help. I have now managed to get it to 
work using Falk’s command. I’ve made a note of your suggestion too, Douglas, 
just in case I have any errors with other subjects.

Best,
Nathan

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

Date: Wednesday, 26 January 2022 at 21:52
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
I think that should work.
One other issue is that the wm.seg.mgz might need to be uchar (a relic
of when computers did not have so much memory). If it does not work with
falk's command, you can try
mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz


On 1/24/2022 2:47 AM, falk.luesebr...@med.ovgu.de wrote:
>  External Email - Use Caution
>
> Oh, sorry... Following the steps from the previous mail you should run this 
> command:
>
>
> mri_mask brain.mgz new_segmentation.mgz wm.seg.mgz
>
>
> Best,
>
> Falk
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von 
> falk.luesebr...@med.ovgu.de 
> Gesendet: Montag, 24. Januar 2022 08:41:15
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
>
>  External Email - Use Caution
>
> Hi Nathan,
>
>
> well, once again, I can't be much of help with regards to your error message. 
> Have you had a look at the data and does it looks reasonable up to that 
> point? Which FreeSurfer version are you running?
>
>
> FreeSurfer needs to have the data in a very specific form. In case of the 
> white matter segmentation the resulting volume should have a value of 110 
> where white matter is located. The SPM segmentation has values of 0 to 1. 
> Therefore, if you would simply try to use that, it wouldn't work. The given 
> command should do that while using the SPM segmentation to mask the 
> brain.mgz. Afterwards, the ventricles and subcortical structures will be 
> filled based on the aseg.presurf.mgz and set to values of 250. The other 
> commands changes the WM segmentation so that the neighbors of all voxels 
> labeled as WM have a face in common - no edges or corners allowed.
>
>
> Best,
>
> Falk
>
>
> 
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von Nathan Kindred (PGR) 
> 
> Gesendet: Freitag, 21. Januar 2022 18:18:14
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
>
>
>  External Email - Use Caution
> Hi Falk,
>
> Thank you, I appreciate your help. By using the convert and mask steps you 
> used I can get through to the -pial stage of autorecon3 before hitting an 
> error (command terminated by signal 11).
> I was wondering about the mri_edit_wm_with_aseg and mri_pretess steps you 
> take though as won’t these essentially overwrite the wm.mgz file so that the 
> SPM segmentation is no longer incorporated? Apologies if I am miss 
> understanding, that is just what appears to happen when I try to replicate 
> those steps (with those included I hit no errors but the outputs are 
> unchanged from before I incorporated the SPM file).
>
> Best,
> Nathan
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of 
> falk.luesebr...@med.ovgu.de 
> Date: Thursday, 20 January 2022 at 07:57
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Using SPM segmentations in FreeSurfer
>  External Email - Use Caution
>
> Hi Nathan,
>
>
> well, I never encountered that error. Therefore, I probably can't be of much 
> help. Anyways, if you provide more details, e.g. which FreeSurfer version you 
> are using, the recon-all.log, and what co