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