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 *Reply-To: *Freesurfer support list 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 *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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