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
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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