or you need to run recon-all -qcache
On 03/17/2017 11:25 AM, Dr. M. Shahid wrote: > 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 <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu>> > *Reply-To: *Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > *Date: *Sunday, March 12, 2017 at 6:56 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 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 > <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 > <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 > <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 > <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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
