Hi Freesurfers, I'm looking at Freesurfer files from are from years ago trying to look at the ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so I'm wondering if there is a way to create it. In trying to find an answer online, I found this: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html I tried that but got an error. It may be a syntax error; this was my command line: recon-all -i /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii MG17_SurferOutput /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
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) MG17 2) recon-all -i /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii MG17_SurferOutput /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ 3) ERROR: Flag /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii unrecognized. /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii MG17_SurferOutput /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with ERRORS at Mon Jan 19 22:27:18 EST 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks so much, Mia _______________________________________________ Freesurfer mailing list [email protected] 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.
