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.limac...@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 <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> > <gr...@nmr.mgh.harvard.edu> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > <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> > <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 > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
