Hi guys, full command line: mri_convert ct.anat.nii ct.anat.mgz command line: ls -l /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii -rw-rw-r-- 1 miaborz acqcash 32506208 Jan 19 22:12 /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
I had to send the ct.anat.nii file separately because it was too large of a file for this email. 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: Tuesday, January 20, 2015 7:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz Hi Mia can you please send us the full command line? And also do an ls -l of that file and include it? thanks Bruce On Tue, 20 Jan 2015, Borzello, Mia wrote: > 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 > > > _______________________________________________ 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.
