I was able to convert your file without problem. When you run mri_convert, you have to give a path to a file that exists. Below, the error says that it cannot find /autofs/space/huygens_001/users/mia/subjects/ct.anat.nii
Does this file exist? It is different than the one you have below, ie /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii On 01/20/2015 11:26 AM, Borzello, Mia wrote: > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
