Hi Mia, try to change the name of the nifti file from ct.ana.nii to ctana.nii. Azeez
> Date: Tue, 20 Jan 2015 11:09:07 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] converting .nii to .mgz > > Does that file exist? > > On 01/19/2015 11:30 PM, 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 > > > > > > -- > 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. >
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