It looks like there's a typo in your recon-all command - there's a space between "-" and autorecon3 .
Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia > Sent: Friday, January 09, 2015 5:30 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. > I attached the output error for recon-all. > > Thanks, > m > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer- > boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, January 08, 2015 4:27 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > did you look in > > /autofs/space/huygens_001/users/mia/subjects > > Can you send us the screen output of recon-all? > > On Thu, 8 Jan 2015, Borzello, > Mia wrote: > > > I looked for that file and did not see a BI22_SurferOutput folder at all. > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > > [fis...@nmr.mgh.harvard.edu] > > Sent: Thursday, January 08, 2015 2:34 PM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] recon-all error > > > > Hi Mia > > > > can you send us the recon-all.log? I don't think you included the > > error message in your email so there isn't much for us to go on. > > > > thanks > > Bruce > > > > On Thu, 8 Jan 2015, Borzello, Mia wrote: > > > >> > >> Hi Freesurfers, > >> > >> I'm wondering if you can help with the following error that occurred > >> when trying to create a reconstruction: > >> > >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 > >> > >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 > >> > >> RedHat release: CentOS release 6.5 (Final) > >> > >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 > >> > >> NMR Center info (/space/freesurfer exists): > >> > >> machine: huygens > >> > >> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects > >> > >> PWD: /autofs/space/huygens_001/users/mia/subjects > >> > >> ssh huygens > >> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects > >> cd /autofs/space/huygens_001/users/mia/subjects > >> > >> > >> 1)BI22 > >> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject > >> BI22_SurferOutput > >> - > i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B > >> I19/4571 > >> /4571157.dcm > >> 3)recon-all -s exited with ERRORS at Thu Jan 8 13:08:33 EST 2015 > >> > >> > >> Thanks, > >> m > >> > >> > > > > _______________________________________________ > > 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.
