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
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