Re: [Freesurfer] Unable to run recon-all

2023-11-17 Thread fsbuild 
External Email - Use Caution

The install location of freesurfer under /usr/local is on purpose read 
only (like the location of most Linux package installs) so you should not be 
trying to process and write subject data there. We provide example 
subjects under /usr/local/freesurfer/7.4.0/subjects for read only purposes.
Neither can you set SUBJECTS_DIR or write files in the process of running 
recon-all to your mounted or shared C drive. This is because the the 
Windows file system does not support creating soft links.
So please try the following. In your Ubuntu linux terminal window, 
go to your HOME directory and create a subjects directory there, i.e., 
you can always read/write to your HOME directory.  Then copy in your 
subject data to be processed there via recon-all and set SUBJECTS_DIR 
appropriately or pass the path on the recon-all command line.
… in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ 
pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your 
data to process for recon-all to live under SUBJECTS_DIR …
It also looks like your license file is not being found. You can set the 
environment variable FS_LICENSE to point to that so it will be found and read,
$ export FS_LICENSE=/home/naiy/license.txt$ head -1 
$fs_license...@somewhere.com    email address 
you used to register
… then try running some Freesurfer commands again …
- R.
On Nov 17, 2023, at 17:49, Nai, Ying Hwey n...@wustl..edu 
wrote:FSissues.txt

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Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

2023-11-17 Thread ludmila 
External Email - Use CautionOh, Good to know! Thank you so so much! Milly M. C. On Nov 17, 2023, at 3:04 PM, Douglas N. Greve  wrote:

  
  
You can't put math or brackets in the contrast file. Just use 
.333 .333 .333 -.333 -.333 -.333 0 0 0 0 


On 11/16/2023 10:50 AM, Ludmila
  Midrigan wrote:


  
  External
  Email - Use Caution
  
Dear
  Douglas, thank you for the reply. 
I
  am attaching it here. I usually create it  (using BASH)  as
  such: <<
   echo
“1 -1” > File_Name.mtx    and
  have never had issues, however I have not used "[ ] " on my
  contrasts before...
Thank
  you so so much for your willingness to help and your time! 


  
  
  
On Wed, Nov 15, 2023 at
  6:47 PM Douglas N. Greve 
  wrote:


   Can you send
/data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx
?
How did you create this file? A lot of word processors will
add special characters that can cause a read failure.

On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:


  External
  Email - Use Caution
  
Hi Douglas, 
Thank you for your
  reply. 
Yes, find attached
  the fsgd file, the contrast is [1 1 1 -1 -1 -1 0 0 0
  0]/3 
As well as the code
  I am running and the whole output from the terminal. 


Thank you so much
  for your help! 
  
  
  
On Thu, Nov 9, 2023 at
  6:35 AM Douglas N. Greve 
  wrote:


   Can you send the command line,
all the terminal output, and your fsgd file?

On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:


  External
  Email - Use Caution
  
Hi dear FS
  experts, 
I am having
  issues with ( I am assuming) the design matrix
  for my GM analysis. 
I am getting
  the error: 


"error:
  MatrixReadTxT: could not scan value [1][1]
  ERROR: loading C Path_to_contrast" 



I am only
  interested in a difference for Group ONE -
  Group ZERO; 
I am trying
  to run a DOSS ( with three groups and 4
  nuisance covariates) 
my
  contrast is : 
[1 1 1 -1 -1
  -1 0 0 0 0]/3 




  I have
standardized all variables. 

Attached is
  the FSGD.xlxs file ( that I did transform into
  a .fsgd file) 
Please let
  me know what I'm doing wrong. 

  Thank you
so much! 
  



  

  
milly mc 


"Life is a
  foreign language; all mispronounce
  it." 

Christopher
  Morley
  

  

  
  
  
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[Freesurfer] license issue with the updated version

2023-11-17 Thread Atena Akbari 
External Email - Use Caution

Dear freesurfer team

I have uninstalled the previous versions of freesurfer on my mac (Sonoma
14.1), and have installed a new version 7.4.1 based on the step by step
freesurfer installation info on the website. I have set the freesurfer home
directory as follows:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1/

export SUBJECTS_DIR=path/to/my/data

source $FREESURFER_HOME/SetUpFreeSurfer.sh


and the license is in the /Applications/freesurfer/7.4.1. But when I run a
freesurfer command I get the following error:


ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt
not found.

QObject::killTimer: Timers cannot be stopped from another thread

QObject::~QObject: Timers cannot be stopped from another thread

/Applications/freesurfer/7.4.1//bin/freeview: line 2:  2938 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"


Could you help me with this issue?


thanks so much.


Best,

Atena
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Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

2023-11-17 Thread Douglas N. Greve 

You can't put math or brackets in the contrast file. Just use
.333 .333 .333 -.333 -.333 -.333 0 0 0 0


On 11/16/2023 10:50 AM, Ludmila Midrigan wrote:


External Email - Use Caution

Dear Douglas, thank you for the reply.
I am attaching it here. I usually create it  (using BASH)  as such: << 
echo “1 -1” > File_Name.mtx and have never had issues, however I have 
not used "[ ] " on my contrasts before...

Thank you so so much for your willingness to help and your time!


On Wed, Nov 15, 2023 at 6:47 PM Douglas N. Greve 
 wrote:


Can you send

/data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx
?
How did you create this file? A lot of word processors will add
special characters that can cause a read failure.

On 11/9/2023 12:33 PM, Ludmila Midrigan wrote:


External Email - Use Caution

Hi Douglas,
Thank you for your reply.
Yes, find attached the fsgd file, the contrast is [1 1 1 -1 -1 -1
0 0 0 0]/3
As well as the code I am running and the whole output from the
terminal.

Thank you so much for your help!

On Thu, Nov 9, 2023 at 6:35 AM Douglas N. Greve
 wrote:

Can you send the command line, all the terminal output, and
your fsgd file?

On 11/3/2023 11:51 AM, Ludmila Midrigan wrote:


External Email - Use Caution

Hi dear FS experts,
I am having issues with ( I am assuming) the design matrix
for my GM analysis.
I am getting the error:

"error: MatrixReadTxT: could not scan value [1][1]
ERROR: loading C Path_to_contrast"

I am only interested in a difference for Group ONE - Group
ZERO;
I am trying to run a DOSS ( with three groups and 4 nuisance
covariates)
my contrast is :
[1 1 1 -1 -1 -1 0 0 0 0]/3

I have standardized all variables.
Attached is the FSGD.xlxs file ( that I did transform into a
.fsgd file)
Please let me know what I'm doing wrong.
Thank you so much!


/milly mc /
/
/
/"Life is a foreign language; all mispronounce it."
/
/Christopher Morley/

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[Freesurfer] Unable to run recon-all

2023-11-17 Thread Nai, Ying Hwey 
External Email - Use Caution

Dear Freesurfer personnel,

I downloaded and installed the latest version successfully following the 
instructions on windows WSL.
However, I could not run recon-all.
I then installed an older version, but I still could not run the recon-all.
Could you please kindly advise me on how to resolve this issue?
Thank you.

Regards,

Ying Hwey




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.
recon-all -s VATPSP-001 -i 
/mnt/c/Users/naiy/Documents/naiy/VATPSP/NIFTI/VATPSP-001/VATPSP-001_M
RI/trans_VATPSP-001_T1.nii -all
mkdir: cannot create directory 
'/usr/local/freesurfer/7.4.0/subjects/VATPSP-001': Permission denied
fs-check-version --s VATPSP-001 --o /tmp/tmp.yht0uH
ERROR: cannot find VATPSP-001
recon-all: version check failed
fs-check-version --s VATPSP-001 --o /tmp/tmp.yht0uH

###:~$ cd HOME
-bash: cd: HOME: No such file or directory
###:~$ cd $HOME
###:~$ ls
Documents  freesurfer_ubuntu20-7.4.0_amd64.deb  
freesurfer_ubuntu22-7.4.1_amd64.deb  fsl  license.txt  matlab
###:~$ cd  /user/local/
-bash: cd: /user/local/: No such file or directory
###:~$ cd  /usr/local/freesurfer/
###:/usr/local/freesurfer$ cp \$HOME/license.txt /usr/local/freesurfer/
cp: cannot stat '$HOME/license.txt': No such file or directory
###:/usr/local/freesurfer$ cp $HOME/license.txt /usr/local/freesurfer/
cp: cannot create regular file '/usr/local/freesurfer/license.txt': Permission 
denied
###:/usr/local/freesurfer$ $FS_LICENSE
/home/naiy/license.txt: line 1: n...@wustl.edu: command not found
/home/naiy/license.txt: line 2: 68956: command not found
/home/naiy/license.txt: line 3: *Cf4wMjQe2ZhQ: command not found
/home/naiy/license.txt: line 4: FSYJ2rnfO8uHU: command not found

###:/usr/local/freesurfer$ cd /usr/local/freesurfer/
###:/usr/local/freesurfer$ ls
7.4.0  license.txt
###:/usr/local/freesurfer$ $FS_LICENSE
/home/naiy/license.txt: line 1: n...@wustl.edu: command not found
/home/naiy/license.txt: line 2: 68956: command not found
/home/naiy/license.txt: line 3: *Cf4wMjQe2ZhQ: command not found
/home/naiy/license.txt: line 4: FSYJ2rnfO8uHU: command not found
###:/usr/local/freesurfer$___
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2023-11-17 Thread Joshua Ezequiel Pasaye 
External Email - Use Caution

Dear Dr. Iglesias,

Thank you for your quick response and insight. I wanted to make sure that there 
were not any specific requirements for the T2w scan when using the segmentation 
command. I will try both and let you know my thoughts.

Kindly,


Joshua E. Pasaye, B.S. (he/him/his)
Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Date: Friday, November 17, 2023 at 2:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of 
the amygdala
Dear Joshua,
This is a bit of an empirical question. I’d totally run both on a few subjects 
and compare the results.
If you do so: I would selfishly/greatly appreciate it if you shared your 
impressions with me :-)
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1AgZJS_lt0DLao4RNJQjdUp6--s94lZQRuhY7Nebh6-r-KlmJo3_XFlRC0kfAa6vzJjeVQXzkeeaH7zelX9kI_IrS8lXLH0j_1vVxwTtbuFhkTFdoSyhIVu89ibzpZeN4YjLlV8qw7HSRnWeTxN16KatsH0eVYzaGfg6bTsLJZ0P773bRtcTT2UTUolqQD8FXD14dl_UyS3EbkyswIGDv8P3j3JOh17S3AoTqZiZWc54POqnTkqUThnCFaD3LiJWA3qzkZHpOzNDR8uKXd0labEq8IuK2ZdP7fS454aGeXwWtqjdKTm9QX_vNEkCTpQQx/http%3A%2F%2Fwww.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joshua Ezequiel Pasaye 

Date: Friday, November 17, 2023 at 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the 
amygdala

External Email - Use Caution
Hello,


I am working on project using Freesurfer’s “Segmentation of hippocampal 
subfields and nuclei of the amygdala” to segment the hippocampal subfields and 
compare it with a software called ASHS developed by the Penn Image Computing 
and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2023-11-17 Thread Iglesias Gonzalez, Juan E. 
Dear Joshua,
This is a bit of an empirical question. I’d totally run both on a few subjects 
and compare the results.
If you do so: I would selfishly/greatly appreciate it if you shared your 
impressions with me :-)
Cheers,
/Eugenio

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joshua Ezequiel Pasaye 

Date: Friday, November 17, 2023 at 11:46 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the 
amygdala

External Email - Use Caution
Hello,


I am working on project using Freesurfer’s “Segmentation of hippocampal 
subfields and nuclei of the amygdala” to segment the hippocampal subfields and 
compare it with a software called ASHS developed by the Penn Image Computing 
and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
​Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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 .
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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

2023-11-17 Thread Joshua Ezequiel Pasaye 
External Email - Use Caution

Hello,


I am working on project using Freesurfer’s “Segmentation of hippocampal 
subfields and nuclei of the amygdala” to segment the hippocampal subfields and 
compare it with a software called ASHS developed by the Penn Image Computing 
and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w 
SPC vNav.08 iso,  ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes 
Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated 
MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to 
run the command: segmentHA_T2.sh  bert  FILE_ADDITIONAL_SCAN   ANALYSIS_ID  
USE_T1  [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal 
sequence so to compare the two outputs, it would be ideal to also use the 
HighRes Hippocampal sequence.



Please let me know if you need additional information.



Thanks,


Joshua E. Pasaye, B.S. (he/him/his)
​Clinical Research Coordinator | Imaging Core
Mesulam Center for Cognitive Neurology and Alzheimer's Disease
Northwestern University – Feinberg School of Medicine
300 E. Superior Street, Tarry 8-734, Chicago, IL 60611
(312) 503-5675 | 
joshua.pas...@northwestern.edu
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[Freesurfer] Hippocampal subfields segmentation

2023-11-17 Thread yunus soleymani 
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Hello Freesurfer users,
I was wondering if there is any Freesurfer code available for performing 
hippocampal subfield segmentation on multiple subjects simultaneously in 
parallel. I already have the code for analyzing a single subject, but I'm 
interested in analyzing hundreds of subjects at once.
Thank you very much.
Best regards,Yunus
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Re: [Freesurfer] recon-all error

2023-11-17 Thread 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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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Transformation of volume images

2023-11-17 Thread Huang, Yujing 
Hi Peter,

Here is an example to convert from native space to MNI305 (fsaverage) in  
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol

  mri_vol2vol --mov orig.mgz
 --targ $FREESURFER_HOME/average/mni305.cor.mgz
 --xfm transforms/talairach.xfm
 --o orig-in-mni305.mgz

In your case, I think you also need ‘—interp nearest’ to convert segmentation.

To convert from fsaverage to native space of a subject, can you try the 
following? I used bert as an example.
 mri_vol2vol
   --mov bert/mri/orig.mgz
   --targ fsaverage/mri/aseg.mgz
   --xfm transforms/talairach.xfm
   --inv
   --o aseg-from-mni305.mgz
   --interp nearest

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of P Pieperhoff
Sent: Thursday, November 16, 2023 12:07 PM
To: Freesurfer support list 
Subject: [Freesurfer] Transformation of volume images


External Email - Use Caution
Dear developers,

please, may I ask you how I can transform volume images (containing discrete 
region labels) from the fsaverage space into the space of a given subject, and 
vice-versa?

I tried the following command:
mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz  --o test_mask.mgz
--s test001  --targ 
test001/mri/orig.mg

or
mri_vol2vol   --interp nearest --mov fsaverage/mri/aseg.mgz  --o test_mask.mgz  
  --targ  test001/mri/T1.mgz  --lta  test001/mri/transforms/talairach.lta --m3z 
talairach.m3z
--s test001

but there was always a large mismatch between the transformed images and the 
target image.

Best regards,
Peter
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