Hi Bruce, Thanks for getting back to me so quickly! I just tried that and got the following error: reading from ct.anat.nii... niiRead(): error opening file /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
I'm wondering if the nifti file is possibly corrupted. Is there a way to check this? Thanks so much, Mia ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, January 19, 2015 10:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz Hi Mia If all you want to do is convert try mri_convert ct.anat.nii ct.anat.mgz Cheers Bruce > On Jan 19, 2015, at 10:33 PM, Borzello, Mia <mborze...@partners.org> wrote: > > 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 > 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.
