Hi,
Your SUBJECTS_DIR environment variable is not set for the subjects you want to analyse, you can either set it on the terminal or inside the fsgd file.
from terminal:-> export SUBJECTS_DIR=/home/limachi/freesurfer/subjects inside fsdg:-> SUBJECTS_DIR /home/limachi/freesurfer/subjects
Best regards,
-- Shahid.
On Wed, Mar 15, 2017 at 7:23 PM, Limachia, Gaurang (NIH/NINDS) [F] < gaurang.limachia@nih.gov> wrote:
This is the output and the subsequent error I receive. How do I run this command (from the tutorial- I already ran –qcached recon-all on my data)
mris_preproc --fsgd gender_age.fsgd \
--cache-in thickness.fwhm10.fsaverage \
--target fsaverage \
--hemi lh \
--out lh.gender_age.thickness.10.mgh
nsubjects = 103
ERROR: cannot find /home/limachi/freesurfer/subjects/CON_202/surf/lh. thickness.fwhm10.fsaverage.mgh
Thanks,
Gaurang
*From: *Douglas Greve greve@nmr.mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Sunday, March 12, 2017 at 6:56 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] subject directory
Can you send the entire terminal output (not just the error)
On 3/10/17 4:01 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
The error is ERROR: cannot find /home/username/freesurfer/ subjects/surf/lh.thickness.fwhm10.fsaverage.mgh
However, the file should run on /servername/username/FATCAT/subjects/…
I don’t know why it tries to find the files in the default home/… folders.
Thanks,
Gaurang
*From: *Douglas Greve greve@nmr.mgh.harvard.edu greve@nmr.mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, March 9, 2017 at 10:45 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] subject directory
can you send the terminal entire output that includes the error?
On 3/9/17 7:57 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
Dear Freesurfer Experts,
I want to customize the directory so I can run the following command
mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
However, after running this command it keeps checking in the wrong directory for the files. How do I change the directory, do I change it in the FSGD file I made or somewhere else? I ran the recon-all qcache, but I need to run this on the previously cached data. I would greatly appreciate it if you can assist me with this problem.
Best Regards,
Gaurang Shyam LImachia
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