Thanks a lot, it works.

just waiting 24 hours.

Best regards,

Carolina

2011/6/10 <rspriti@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.

--