Hi Carolina, -subject is not recognized by Freesurfer...Use -subjid or -s instead.
setenv SUBJECTS_DIR <path to tutorial data> recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to freesurfer recons>/hptu_subj001 Priti > Hello Freesurfer's users, > > I'm starting using FS and I have a problem running recon-all > I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within > tutorial_subj > First I convert nii.gz to mgz qith the command: > recon-all -i MPRAGE.nii.gz -s hptu_subj001 > and then in order to process all, I type: > recon-all i 001.mgz subject hptu_subj001 all > > cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> > recon-all i 001.mgz subject hptu_subj001 all > ERROR: Flag i unrecognized. > i 001.mgz subject hptu_subj001 all > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae > #50-Ubuntu > SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux > > recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 > > then I tried with: > > cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> > recon-all i MPRAGE.nii.gz subject hptu_subj001 all > ERROR: Flag i unrecognized. > i MPRAGE.nii.gz subject hptu_subj001 all > Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae > #50-Ubuntu > SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux > > recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 > > How I can fix this error? > > Thanks a lot, > > Best regards, > > Carolina > _______________________________________________ > 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.