Also, i didn't attach the error I got- please see attached. Thanks! m ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, January 20, 2015 4:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] converting .nii to .mgz
It was initially in the wrong folder, but now it in the mri folder. ls -l /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz -rw-rw-r-- 1 miaborz acqcash 15954217 Jan 20 16:16 /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz Still unable to load with tkmedit though. Thanks, m ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, January 20, 2015 3:51 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] converting .nii to .mgz does /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz exist? On 01/20/2015 03:40 PM, Borzello, Mia wrote: > Okay, cool, I just tried with the full path to the .nii file and it worked. > However, when I tried to load the ct.anat.mgz using tkmedit i get an error in > loading the volume. > > 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) tkmedit MG17_SurferOutput norm.mgz lh.pial -aux ct.anat.mgz > 3) this is the error: > mghRead(/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.mgz, > -1): could not open file > Converting main surface: 100% done. > Converting main surface: 100% done. > Converting original surface: 100% done. > Converting pial surface: 100% done. > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_common.tcl > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkm_wrappers.tcl > Reading /usr/local/freesurfer/stable5_3_0/lib/tcl/fsgdfPlot.tcl > Reading /usr/local/freesurfer/stable5_3_0/tktools/tkUtils.tcl > > and the grey box pops up saying it couldn't load the volume. > > (not sure if I should start a new thread for this or not). Thanks again for > all your help, > m > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, January 20, 2015 2:57 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] converting .nii to .mgz > > 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 > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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