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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer