[Freesurfer] tracula quality assessment dwi_motion.txt units

[Ruth Carper]

What are the units of measure for translation and rotation as output in the 
dwi_motion.txt file from Tracula? It's not stated in the output file or on the 
page http://freesurfer.net/fswiki/FsTutorial/TraculaOutputsI would have assumed 
mm and degrees, but the rotation values are consistently less than 0.01, which 
doesn't seem likely.
--Ruth
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Re: [Freesurfer] recon -all errors

[Jasmin Alves]

Bruce,

Sorry to be a pain, but for some reason, I cannot still get recon-all to
work.

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya -all &

[1] 14655

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: SUBJECTS_DIR
/Desktop/Brain_Child_subs does not exist.

Thanks,

Jasmin

On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl 
wrote:

> Hi Jasmin
>
> you need a '-' sign first. It should be:
>
> recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \
> joya -all &
>
> cheers
> Bruce
>
>
> On Mon, 25 Jan 2016, Jasmin Alves wrote:
>
> Hi Bruce,
>> Thanks for the reply, I attempted to direct Subjects_dir to the folder
>> with
>> my data but I received the following error.
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
>> SUBJECTS_DIR=/Desktop/Brain_Child_subs
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
>> /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &
>>
>> [1] 13867
>>
>> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
>> unrecognized.
>>
>> -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all
>>
>> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
>> Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016
>>
>> Thanks so much,
>>
>> Jasmin
>>
>>
>> On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jasmin
>>
>>   you  need to create a directory where you have write permission
>>   and room for the subject reconstruction to be written to, then
>>   set the SUBJECTS_DIR environment variable to point to it. At the
>>   moment you are trying to use the subject directory we
>>   distribute, which is in some system (and read-only) location.
>>   You can do this on the command line of recon-all via:
>>
>>   recon-all -sd  ...
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Sun, 24 Jan 2016, Jasmin Alves wrote:
>>
>>   Hello Freesurfer,
>>
>>   I am trying to learn freesurfer and ran into the following
>>   issues below
>>   running the recon -all command.
>>
>>   FREESURFER_HOME: /Applications/freesurfer
>>
>>   Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   Kernel info: Darwin 14.5.0 x86_64
>>
>> 1)
>>
>>   joya
>>
>>2)
>>
>>Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
>>   T1_original_joya.nii
>>   -subject joya -all &
>>
>>
>>   3)
>>
>>   [1] 12300
>>
>>   Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
>>   /Applications/freesurfer/subjects/joya: Permission denied
>>
>>   mkdir: /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   mkdir: /Applications/freesurfer/subjects/joya/scripts:
>>   Permission denied
>>
>>   cp:
>>   /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   cat:
>>   /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
>>   No such
>>   file or directory
>>
>>   INFO: FreeSurfer build stamps do not match
>>
>>   Subject Stamp:
>>
>>   Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>
>>   INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
>>
>>   Actual FREESURFER_HOME /Applications/freesurfer
>>
>>   /Applications/freesurfer/subjects/joya: No such file or
>>   directory.
>>
>>
>>   [1]+  Exit 1  recon-all -i
>>   T1_original_joya.nii -subject
>>   joya -a
>>
>>   Thank you,Jasmin
>>
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
>> ___
>> Freesurfer mailing list
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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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>> --
>> Jasmin AlvesPredoctoral Student
>> Medical Biology Graduate Program
>> University of Southern California
>> jal...@usc.edu
>>
>>
>>
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> The information in this e-mail is intended only for the person to whom it
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> addressed. If 

Re: [Freesurfer] recon -all errors

[Bruce Fischl]

Hi Jasmin

you need a '-' sign first. It should be:

recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject \
joya -all &

cheers
Bruce

On Mon, 25 Jan 2016, Jasmin Alves 
wrote:



Hi Bruce, 
Thanks for the reply, I attempted to direct Subjects_dir to the folder with
my data but I received the following error. 

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export
SUBJECTS_DIR=/Desktop/Brain_Child_subs

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd
/Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all &

[1] 13867

Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all
unrecognized.

-sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all

Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue
Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016

Thanks so much,

Jasmin


On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl 
wrote:
  Hi Jasmin

  you  need to create a directory where you have write permission
  and room for the subject reconstruction to be written to, then
  set the SUBJECTS_DIR environment variable to point to it. At the
  moment you are trying to use the subject directory we
  distribute, which is in some system (and read-only) location.
  You can do this on the command line of recon-all via:

  recon-all -sd  ...

  cheers
  Bruce


  On Sun, 24 Jan 2016, Jasmin Alves wrote:

  Hello Freesurfer,

  I am trying to learn freesurfer and ran into the following
  issues below
  running the recon -all command. 

  FREESURFER_HOME: /Applications/freesurfer

  Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  Kernel info: Darwin 14.5.0 x86_64

    1) 

  joya

   2) 

   Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i
  T1_original_joya.nii
  -subject joya -all &


  3)

  [1] 12300 

  Jasmins-MacBook-Pro:subjects jasminalves$ mkdir:
  /Applications/freesurfer/subjects/joya: Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  mkdir: /Applications/freesurfer/subjects/joya/scripts:
  Permission denied

  cp:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  cat:
  /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt:
  No such
  file or directory

  INFO: FreeSurfer build stamps do not match

  Subject Stamp: 

  Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

  INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects

  Actual FREESURFER_HOME /Applications/freesurfer

  /Applications/freesurfer/subjects/joya: No such file or
  directory.


  [1]+  Exit 1                  recon-all -i
  T1_original_joya.nii -subject
  joya -a

  Thank you,Jasmin

Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 



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--
Jasmin AlvesPredoctoral Student 
Medical Biology Graduate Program 
University of Southern California
jal...@usc.edu 


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Re: [Freesurfer] Incomplete output

[Bruce Fischl]

Hi Maryam

can you send us some images so we can see what you mean?
Bruce
On Tue, 26 Jan 
2016, maryam koochaki wrote:



Dear experts,
I am kind of new at working with freesurfer.
recon-all process has completed without error, but when I look at brainmask
volume on freeview, one of the issues is that lateral ventricle is
completely excluded. I have tried to edit it with editing the white matter
volume, but no success so far. I do not know how to correct it. Have anybody
here had the same issue?
 
Thanks,
Maryam







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[Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

[Alshikho, Mohamad J.]

Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize 
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and 
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by 
flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an 
output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. 
Now After segmenting the brain stem. I see that the Ventral DC belongs to the 
mid brain.

Is this natural?


Thanks in advance for any suggestion!

Mohamad
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Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

[Eugenio Iglesias]

Dear Mohamad, 
The brainstem module uses different anatomical definitions than aseg/wmparc, 
and yes, the largest discrepancy is in the midbrain. 
For the midbrain, I like the segmentation from the brainstem module better, 
since it is based on manual annotations made by UCSF collaborators working 
explicitly on the brainstem regions. But Bruce's opinion might be different? 
Cheers, 
/Eugenio 



Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Mohamad J. Alshikho"  
To: "Freesurfer support list"  
Sent: Tuesday, January 26, 2016 4:05:24 PM 
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed} 

Dear Freesurfers, 
After segmenting the brain stem using FS6 tools. I used Free view to visualize 
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and 
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by 
flipping the images. 
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an 
output of brain stem segmentation). 
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. 
Now After segmenting the brain stem. I see that the Ventral DC belongs to the 
mid brain. 

Is this natural? 


Thanks in advance for any suggestion! 

Mohamad 

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Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

[Bruce Fischl]

nope, I agree completely. Brainstem and ventralDC and such were never 
very well-defined by the CMA, which is what our original manual labels 
were based on. Eugenio's stuff is a significant improvement
Bruce
On Tue, 26 Jan 
2016, Eugenio Iglesias wrote:

> Dear Mohamad,
> The brainstem module uses different anatomical definitions than aseg/wmparc,
> and yes, the largest discrepancy is in the midbrain.
> For the midbrain, I like the segmentation from the brainstem module better,
> since it is based on manual annotations made by UCSF collaborators working
> explicitly on the brainstem regions. But Bruce's opinion might be different?
> Cheers,
> /Eugenio
> 
> 
> 
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> 
> 
> From: "Mohamad J. Alshikho" 
> To: "Freesurfer support list" 
> Sent: Tuesday, January 26, 2016 4:05:24 PM
> Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}
> 
> Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used
> Free view to visualize the final images. In Free view I opened "orig.mgz",
> "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the
> segmented structures by flipping the images.
> I noticed an overlap between Ventral DC ( left and right) and mid brain ( as
> an output of brain stem segmentation).
> I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different
> segments. Now After segmenting the brain stem. I see that the Ventral DC
> belongs to the mid brain.
> 
> Is this natural?
> 
> 
> Thanks in advance for any suggestion!
> 
> Mohamad
> 
> ___
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> 
> 
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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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
>
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Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

[Alshikho, Mohamad J.]

Bruce and Juan,
Thanks a lot for your quick answer. I have one more question please:

What are the anatomical definitions that the brain stem module uses in order to 
segment the brain stem. If you can point me to a reference that can help me to 
understand this point this will be great!!

Thanks again





From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu]
Sent: Tuesday, January 26, 2016 10:16 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Dear Mohamad,
The brainstem module uses different anatomical definitions than aseg/wmparc, 
and yes, the largest discrepancy is in the midbrain.
For the midbrain, I like the segmentation from the brainstem module better, 
since it is based on manual annotations made by UCSF collaborators working 
explicitly on the brainstem regions. But Bruce's opinion might be different?
Cheers,
/Eugenio



Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


From: "Mohamad J. Alshikho" 
To: "Freesurfer support list" 
Sent: Tuesday, January 26, 2016 4:05:24 PM
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

Dear Freesurfers,
After segmenting the brain stem using FS6 tools. I used Free view to visualize 
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and 
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by 
flipping the images.
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an 
output of brain stem segmentation).
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. 
Now After segmenting the brain stem. I see that the Ventral DC belongs to the 
mid brain.

Is this natural?


Thanks in advance for any suggestion!

Mohamad

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Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed}

[Eugenio Iglesias]

Here it is (open access) 
http://www.sciencedirect.com/science/article/pii/S1053811915001895 




Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Mohamad J. Alshikho"  
To: "Freesurfer support list"  
Sent: Tuesday, January 26, 2016 4:25:35 PM 
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed} 

Bruce and Juan, 
Thanks a lot for your quick answer. I have one more question please: 

What are the anatomical definitions that the brain stem module uses in order to 
segment the brain stem. If you can point me to a reference that can help me to 
understand this point this will be great!! 

Thanks again 





From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias 
[e.igles...@bcbl.eu] 
Sent: Tuesday, January 26, 2016 10:16 AM 
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed} 

Dear Mohamad, 
The brainstem module uses different anatomical definitions than aseg/wmparc, 
and yes, the largest discrepancy is in the midbrain. 
For the midbrain, I like the segmentation from the brainstem module better, 
since it is based on manual annotations made by UCSF collaborators working 
explicitly on the brainstem regions. But Bruce's opinion might be different? 
Cheers, 
/Eugenio 



Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Mohamad J. Alshikho"  
To: "Freesurfer support list"  
Sent: Tuesday, January 26, 2016 4:05:24 PM 
Subject: [Freesurfer] Brain stem segmentation in Freesurfer 6 {Disarmed} 

Dear Freesurfers, 
After segmenting the brain stem using FS6 tools. I used Free view to visualize 
the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and 
"brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by 
flipping the images. 
I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an 
output of brain stem segmentation). 
I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. 
Now After segmenting the brain stem. I see that the Ventral DC belongs to the 
mid brain. 

Is this natural? 


Thanks in advance for any suggestion! 

Mohamad 

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dispose of the e-mail. 

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Re: [Freesurfer] Crashing with Fedora 23

[Barron, Daniel]

Hi ZK,
It was SLED 11.4. Thanks for looking into it. Appreciate your time.
db

On 1/26/16, 11:04 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Z K"  wrote:

>This appears to be something specific with Fedora 23... I will attempt
>to duplicate on a Fedora 23 virtual machine as I dont have one handy.
>Can you recall what version you were running before you upgraded to
>Fedora 23 when recon-all when running successfully?
>
>On 01/25/2016 02:05 PM, Barron, Daniel wrote:
>> Hi Martin,
>> We¹ve got the tcsh installed and seems to be working.  Can¹t find a
>> similar report on the list serve, so I¹ve attached the bug report info
>> below plus the orig_nu.log output, which is where the script is
>> crashing. Please help!
>> Cheers,
>> Daniel
>>
>> *Output from buggr:*
>> FREESURFER_HOME: /home/freesurfer
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> RedHat release: Fedora release 23 (Twenty Three)
>> Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64
>> Subject Name: 2_03T_N12_12_18441
>>
>> *Command I¹m entering:*
>> for subject in 2_03T_N12_12_18441; do
>> recon-all -subjid ${subject} -all -hippo-subfields
>> done
>>
>> *Error Message (from recon-all.error):*
>> --
>> SUBJECT 2_03T_N12_12_18441
>> DATE Mon Jan 25 18:40:30 GMT 2016
>> USER dsbarron
>> HOST psyws26.psych.ox.ac.uk
>> 
>>>uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74=>
>> PROCESSOR x86_64
>> OS Linux
>> Linux psyws26.psych.ox.ac.uk
>> 
>>>uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>> /home/freesurfer/bin/recon-all
>> PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri
>> CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>> --no-rescale --i orig.mgz --o orig_nu.mgz
>>
>> #
>> *recon-all.log:*
>>
>> Mon Jan 25 18:43:18 GMT 2016
>> /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441
>> /home/freesurfer/bin/recon-all
>> -subjid 2_03T_N12_12_18441 -all -hippo-subfields
>> subjid 2_03T_N12_12_18441
>> setenv SUBJECTS_DIR /home/dsbarron/Schmidt/Freesurfer
>> FREESURFER_HOME /home/freesurfer
>> Actual FREESURFER_HOME /home/freesurfer
>> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> Linux psyws26.psych.ox.ac.uk
>> 
>>>uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74=> 4.3.3-300.fc23.x86_64
>> #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>> cputime  unlimited
>> filesize unlimited
>> datasize unlimited
>> stacksize8192 kbytes
>> coredumpsize 0 kbytes
>> memoryuseunlimited
>> vmemoryuse   unlimited
>> descriptors  1024
>> memorylocked 64 kbytes
>> maxproc  128183
>> maxlocks unlimited
>> maxsignal128183
>> maxmessage   819200
>> maxnice  0
>> maxrtprio0
>> maxrttimeunlimited
>>
>>totalusedfree  shared  buff/cache
>> available
>> Mem:   32901484 2311624 1288116  12189629301744
>> 29874168
>> Swap:  16515068 134492415170144
>>
>> 
>> program versions used
>> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
>> $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
>> mri_convert -all-info
>> ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion:
>> $Name: stable5 $  TimeStamp: 2016/01/25-18:43:18-GMT  BuildTimeStamp:
>> May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05
>> 21:55:16 mreuter Exp $  User: dsbarron  Machine: psyws26.psych.ox.ac.uk
>> 
>>>uk=AwMFaQ=-dg2m7zWuuDZ0MUcV7Sdqw=g50p1nyHibMCglONMxU9nWo8J4gdlxnC0y
>>h34fYFosM=bGlcZ8MfX80JSvJjpVUHhgBmIkHjEWVW4RdH88hoqAI=gsKhS9Mym34PR3U
>>Xiv5lzMEopfAGkdYdn_1AEwRrd74=>Platform:
>> Linux  PlatformVersion: 4.3.3-300.fc23.x86_64  CompilerName: GCC
>> CompilerVersion: 40400
>> FLIRT version 5.5
>> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
>> mri_convert --version
>> stable5
>> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
>> ProgramVersion: $Name: stable5 $  TimeStamp: 2016/01/25-18:43:19-GMT
>> BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: 

Re: [Freesurfer] Qdec ROI Analysis

[Douglas N Greve]

If all you want are the stats from Desikan/Destrieux, then use the 
provided stats files and load them into SPSS (or whatever). That note 
has to do with if you have your own ROI from which you want statistics.
doug

On 01/25/2016 09:47 PM, Larissa McKetton wrote:
> Dear Freesurfer community,
>
> I am working on an ROI analysis using qdec. I have created all aseg 
> and aparc stats files and would like to determine if there are any 
> differences in volume, surface area, and thickness for certain 
> structures between two groups. I was wondering with the analysis, 
> would it be okay to use the resulting aseg/aparc output stats from 
> either the Desikan/Destrieux atlases and run these values through SPSS 
> or is it better to draw ROI labels on the fsaverage brain, apply the 
> label to each subject, and run the analyses this way. I am asking 
> because the following tutorial states:
>
> *"Note*: If you want to use a pre-existing label and register it to 
> fsaverage, be aware that this might involve two instances of 
> resampling and the results might not be as accurate as they would be 
> if you drew the label on fsaverage. Please contact the FreeSurfer team 
> to get more details on this process if you have any concerns."
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#TableoftheaveragethicknessofeachcorticalparcellationintheDestrieuxatlas
>
> If drawing labels on the fsaverage brain and applying them to each 
> subject is the way to go- would I need to correct for multiple 
> comparisons?
>
> Many thanks,
> Larissa
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] DESPOT T1 map

[Worker, Amanda]

Hi All,


I have a T1 map which has been synthesised from a DESPOT imaging sequence and I 
am hoping to use this as input to recon-all. Do you know if this will be 
possible at all, or if there is anything I can do to prepare the T1 map to run 
through recon-all?


Thanks in advance,


Amanda
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Re: [Freesurfer] DESPOT T1 map

[Bruce Fischl]

Hi Amanda


if it is a T1 map then it will have inverse contrast from what we 
expect. If you have a PD map also you can run them through mri_synthesize 
to apply the Bloch equations to synthesize a T1-weighted image (e.g. with a 
flip angle of 30).


cheers
Bruce


On Tue, 26 Jan 2016, Worker, Amanda wrote:



Hi All,


I have a T1 map which has been synthesised from a DESPOT imaging sequence
and I am hoping to use this as input to recon-all. Do you know if this will
be possible at all, or if there is anything I can do to prepare the T1 map
to run through recon-all?


Thanks in advance,


Amanda


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[Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[John Plass]

Hello,
I've been following the Ex-Vivo Recon instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan
of a formalin-fixated brain. With considerable manual editing, I've been
able to produce convincing white and pial surfaces, but I am having trouble
getting a good parcellation. The labels are reversed from anterior to
posterior (e.g., superior parietal lobule area is labelled as middle
frontal gyrus). I am assuming this has to do with problems with the surface
registration. Also, when viewing the surfaces in Freeview, they appear
pretty dark (perhaps similar to
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.html),
although the correspondence between red/green and gyri and sulci appears to
be correct. Might this be part of the problem?

Any advice would be much appreciated! If you'd like to take a look at the
files, please let me know what and where to upload.

Thanks very much for your help.

Best regards,
John Plass
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Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Dear Doug,

Thanks for your reply. Is it possible to upload the raw DICOM to a server
so that you can see if mri_convert is making the orientation in the output
NII file neurological? I just want to make sure what my image orientation
is and how mri_convert interacts with it.

Many thanks!
Daniel


-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/25/16, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"  wrote:

>not necessarily. For FSL, the determinant must be less than 0 (see
>mri_info output). Having said that, even if the det<0, it may still show
>up funny in fslview
>
>On 01/25/2016 12:11 PM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> I find that mri_convert will convert DICOM of structural scan to
>> neurological orientation by default.
>>
>> For example, mri_convert --in_type dicom --out_type mii > the DICOM directory> 
>>
>> Thus, the NII may need to be swapped in x for use in FSL.
>>
>> In this the case?
>>
>> Many thanks,
>> Daniel
>>
>> -- 
>> Daniel Yang, Ph.D.
>> Yale Child Study Center
>> E-mail: daniel.yj.y...@yale.edu
>>
>>
>> ___
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>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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Re: [Freesurfer] mri_convert and image orientation

[Douglas N Greve]

If the determinant is less than 0, then it is radiological (probably it 
will be radiological).

On 01/26/2016 04:20 PM, Yang, Daniel wrote:
> Dear Doug,
>
> Thanks for your reply. Is it possible to upload the raw DICOM to a server
> so that you can see if mri_convert is making the orientation in the output
> NII file neurological? I just want to make sure what my image orientation
> is and how mri_convert interacts with it.
>
> Many thanks!
> Daniel
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] recon-all: core dumped error

[Bruce Fischl]

Hi Fengji

this is a known bug in mris_parcellate. We can give you an updated version 
if you want, but you should probably rerun all your subjects using it. The 
good news is that it's fast - just a couple of min/hemi


cheers
Bruce
 On Tue, 26 Jan 
2016, Fengji Geng wrote:



Hello fs experts,

We ran a command like ´recon-all -all -s HMN002 -hippocampal-subfields-T1T2
HMN002/T2/*.mgz T1T2´. Then, there was an error as ´Abort (core dumped)´
(which is also attached below). The error log file is also attached here. 

Error msg:
---
--
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $
reading atlas 
from/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.fille
d.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file
average std = 1.0   using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1592 labels changed using aseg
relabeling using gibbs priors...
000:   2975 changed, 134786 examined...
001:    698 changed, 12707 examined...
002:    152 changed, 3873 examined...
003: 50 changed, 880 examined...
004: 29 changed, 284 examined...
005: 16 changed, 164 examined...
006:  7 changed, 87 examined...
007:  1 changed, 42 examined...
008:  0 changed, 4 examined...
206 labels changed using aseg
000: 105 total segments, 64 labels (264 vertices) changed
001: 43 total segments, 4 labels (14 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
1 filter iterations complete (10 requested, 0 changed)
Abort (core dumped)
Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23
12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016

Our freesurfer information:
 freesurfer-Linux-centos6_x86_64-dev-20151215 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /cell_root/software/freesurfer/dev/sys
FSFAST_HOME   /cell_root/software/freesurfer/dev/sys/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /export/data/hippocampus/HMN/data
MNI_DIR   /cell_root/software/freesurfer/dev/sys/mni
FSL_DIR   /cell_root/software/fsl/new/sys

Looking forward to hearing how we can resolve this error. Also, thanks in
advance.

Best,

- Fengji


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Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[Bruce Fischl]

Hi John

does it come up in the correct orientation in freeview? If you didn't 
scan it in the orientation that a person would have been lying in the 
scanner, you will need to reorient the data so that we know what e.g. 
anterior is

cheers
Bruce

On Tue, 26 Jan 2016, John Plass wrote:

> Hello,
> I've been following the Ex-Vivo Recon instructions
> https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan
> of a formalin-fixated brain. With considerable manual editing, I've been
> able to produce convincing white and pial surfaces, but I am having trouble
> getting a good parcellation. The labels are reversed from anterior to
> posterior (e.g., superior parietal lobule area is labelled as middle frontal
> gyrus). I am assuming this has to do with problems with the surface
> registration. Also, when viewing the surfaces in Freeview, they appear
> pretty dark (perhaps similar 
> tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
> l), although the correspondence between red/green and gyri and sulci appears
> to be correct. Might this be part of the problem?
> 
> Any advice would be much appreciated! If you'd like to take a look at the
> files, please let me know what and where to upload.
> 
> Thanks very much for your help.
> 
> Best regards,
> John Plass
> 
>
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Re: [Freesurfer] Ex-Vivo Brain: Dark Surface in Freeview; Bad Surface Registration

[John Plass]

Hi Bruce,
Thanks for your reply. The orientation is correct in freeview, although,
digging further, I see that that it is misoriented when I view it in
tkregister2. I ran tkregister --mgz --s {subID} --fstal --surf orig, and
the orig volume is shown oriented correctly, but the orig surface appears
to have some of the dimensions swapped. Any idea why this might be?

Thanks for your help!

John

On Tuesday, January 26, 2016, Bruce Fischl 
wrote:

> Hi John
>
> does it come up in the correct orientation in freeview? If you didn't
> scan it in the orientation that a person would have been lying in the
> scanner, you will need to reorient the data so that we know what e.g.
> anterior is
>
> cheers
> Bruce
>
> On Tue, 26 Jan 2016, John Plass wrote:
>
> > Hello,
> > I've been following the Ex-Vivo Recon instructions
> > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE
> scan
> > of a formalin-fixated brain. With considerable manual editing, I've been
> > able to produce convincing white and pial surfaces, but I am having
> trouble
> > getting a good parcellation. The labels are reversed from anterior to
> > posterior (e.g., superior parietal lobule area is labelled as middle
> frontal
> > gyrus). I am assuming this has to do with problems with the surface
> > registration. Also, when viewing the surfaces in Freeview, they appear
> > pretty dark (perhaps similar tohttps://
> mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
> > l), although the correspondence between red/green and gyri and sulci
> appears
> > to be correct. Might this be part of the problem?
> >
> > Any advice would be much appreciated! If you'd like to take a look at the
> > files, please let me know what and where to upload.
> >
> > Thanks very much for your help.
> >
> > Best regards,
> > John Plass
> >
> >
> ___
> Freesurfer mailing list
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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 Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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-- 

---
John Plass
Ph.D. Candidate
Visual Perception, Neuroscience, and Cognition Lab
Northwestern University
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Re: [Freesurfer] Cannot open FreeSurfer application zipped file

[Meirelles, Osorio (NIH/NIA/IRP) [E]]

Hi Lee,

   I ran the command " sha1sum 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result  
7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 
0c8d784e28a435bd5ea45be6a461990894cfc5b7  , according to the webpage:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt

   So does this mean that I have a Freesurfer  corrupted installation file?  
What would you recommend?  Can you suggest me a link to download a  more 
updated version? 

  Thanks,

  Osorio

-Original Message-
From: Meirelles, Osorio (NIH/NIA/IRP) [E] 
Sent: Monday, December 28, 2015 2:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Lee,

 I guess it worked.   It looks like several hundreds  of files were unzipped., 
however, in the end, there was still the following message:

gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

At this stage I do not know if this is a minor error or if there were many more 
files to be unzipped that were not since the process was interrupted.

 What would you recommend I do next?

Thank you,

Osorio

-Original Message-
From: Lee Tirrell [mailto:ltirr...@nmr.mgh.harvard.edu] 
Sent: Monday, December 28, 2015 1:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Osorio,

Are you sure the file completely downloaded without errors? You can confirm 
this by running:

sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

The output of this command should match the result on this webpage:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt

If your file is uncorrupted, try running this command to unzip it:

tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Best,
Lee

On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:

> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Meirelles, Osorio (NIH/NIA/IRP) [E]
> Sent: Thursday, December 24, 2015 12:23 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: RE: [Freesurfer] hello freesurfer developer~
>
> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 24, 2015 12:16 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: Re: [Freesurfer] hello freesurfer developer~
>
> Hi A-reum
>
> you should probably ask the Wash U HCP group. I'll cc Matt Glasser who
> might be able to answer your question
> cheers
> Bruce
>
> On Thu, 24 Dec 2015, A-reum Min wrote:
>
>> hello experts!my name is areum.
>> i have some question to you.
>> a few days ago i was down load HCP(human connectom project) data.
>> but.. how can i use these HCP format.
>> i have never seen before these format(fig.1.png)
>> I want to see HCP data subjects's cortical thickness using qdec.
>> how can i to do? 
>> plz answer me  
>>
>> 2015-11-10 7:49 GMT+09:00 A-reum Min :
>>   Hello experts!
>> I have some question to you..
>>
>> I don't need to show up so small blue regions(fig.1 blue region)
>>
>> How can i control these? 
>>
>> 2015-11-10 7:41 GMT+09:00 Douglas N Greve :
>>   Hi, please create a new thread since this is a new topic.
>>   Also, I don't
>>   understand your question so please elaborate.
>>
>>   On 11/09/2015 05:34 AM, A-reum Min wrote:
>>  > Hello experts!
>>  >
>>  > i have some question to you..
>>  >
>>  > How can i control the cluster size?
>>  >
>>  > My cluster threshold is 1.
>>  >
>>  > then, too many blue regions (as shown fig.1).
>>  >
>>  > so, i want to control cluster threshold 1--> cluster
>>   threshold 5.
>>  >
>>  > 2015-11-08 20:44 GMT+09:00 A-reum Min
>>   

Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so
it’s most likely to be radiological.

Just curious, so determinant > 0 means neurological then?

Daniel


-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve"  wrote:

>If the determinant is less than 0, then it is radiological (probably it
>will be radiological).
>
>On 01/26/2016 04:20 PM, Yang, Daniel wrote:
>> Dear Doug,
>>
>> Thanks for your reply. Is it possible to upload the raw DICOM to a
>>server
>> so that you can see if mri_convert is making the orientation in the
>>output
>> NII file neurological? I just want to make sure what my image
>>orientation
>> is and how mri_convert interacts with it.
>>
>> Many thanks!
>> Daniel
>>
>>
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>contains patient information, please contact the Partners Compliance
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>error
>but does not contain patient information, please contact the sender and
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>


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