Hi Carolina, Sorry My bad. I was inaccurate in my previous message.
-subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > 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 > > > _______________________________________________ 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.
