Thanks a lot, it works. just waiting 24 hours. Best regards,
Carolina 2011/6/10 <rspr...@nmr.mgh.harvard.edu> > 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 > > > > > > > > > > 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. > > --
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