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>
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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