can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > *Hello freesurfer* > > *Sorry for the personal message Shantanu. * > > *I managed to convert my dicom to nifti using mricron software, though had > to make some changes to the preferences. * > > *About the dcmunpack: The user manual on dcmunpack on fs site says that > the > unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips > infinity for our PET scan.* > > *I am very new to Unix, free surfer and neuroimaging, so couldn't > understand what nipy would do...* > > *My FS is working fine as when I typed tkmedit bert orig.mngz for volume > view it was displaying image.* > > *But the when I tried to convert my .nii files to .mgz format , I get the > following error:* > > > Last login: Tue May 6 10:40:32 on ttys000 > dhcp020-222-117:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > dhcp020-222-117:~ sampada$ mri_convert > '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > '/Users/sampada/Desktop/test/mri/org/.mgz' > mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii > /Users/sampada/Desktop/test/mri/org/.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... > TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (0.0268034, -0.99958, 0.0110098) > j_ras = (0.0381548, 0.0120287, 0.999199) > k_ras = (0.998912, 0.0263618, -0.0384612) > writing to /Users/sampada/Desktop/test/mri/org/.mgz... > mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open > file > > ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz > > > *Will you please let me know what command I need to use to mri convert and > recon all of my files? * > I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 > (in the order of the acquisition acquired at the time of experiment).* > > > *Thanks and regards,* > > *Sampada* > > > > > > On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu >> wrote: > >> >> Have you tried using dcmunpack? You run it twice, once without any >> output to get a list of runs in the folder. The 2nd with how you want >> the data converted. Run it with --help to get more info >> doug >> >> On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: >> > Hello I have only recently started the fmri data analysis and I >> > downloaded freesurfer point by point from martinos site and >> > incorporated the license file as well into the Applications/freesurfer >> > directory. I have run into the first problem and that is of data >> > conversion. My file is in dcm format and I have 11,000 dcm files to >> > convert. However, before I was using Jamaan Alghamadi created gui and >> > it is not able to convert the mri dcm files. Then I shifted to UNIX >> > and again it is saying error. >> > >> > My file is on the desktop and I have given it subject id as Grace. My >> > directory to the dcm file is '/Users/sampada/desktop/Grace. >> > >> > My terminal look like this before I proceed with the file conversion >> > >> > Last login: Mon Apr 28 15:10:13 on ttys001 >> > >> > dhcp020-223-179:~ sampada$ export >> FREESURFER_HOME=/Applications/freesurfer >> > >> > dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> > >> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >> > >> > Setting up environment for FreeSurfer/FS-FAST (and FSL) >> > >> > FREESURFER_HOME /Applications/freesurfer >> > >> > FSFAST_HOME /Applications/freesurfer/fsfast >> > >> > FSF_OUTPUT_FORMAT nii.gz >> > >> > SUBJECTS_DIR /Applications/freesurfer/subjects >> > >> > MNI_DIR /Applications/freesurfer/mni >> > >> > >> > >> > Will anyone please let me know what I am doing wrong? I will be very >> > grateful for any input. >> > >> > >> > Thanks and regards, >> > >> > >> > Sampada >> > Senior research support specialist >> > Molecular and neuroimaging department >> > Department of Psychiatry >> > 451, biomedical research building >> > University at Buffalo (south campus) >> > Buffalo, NY-14216 >> > >> > >> > >> > >> > >> > _______________________________________________ >> > 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. >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
