Re: [Freesurfer] subject directory

or you need to run recon-all -qcache

On 03/17/2017 11:25 AM, Dr. M. Shahid wrote:

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 mailto: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
<mailto:greve@nmr.mgh.harvard.edu>>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Date: *Sunday, March 12, 2017 at 6:56 PM


*To: *"freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu
<mailto: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>
    <mailto:greve@nmr.mgh.harvard.edu>
    *Reply-To: *Freesurfer support list
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    *Date: *Thursday, March 9, 2017 at 10:45 PM
    *To: *"freesurfer@nmr.mgh.harvard.edu"
    <mailto:freesurfer@nmr.mgh.harvard.edu>
    <freesurfer@nmr.mgh.harvard.edu>
    <mailto: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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