Hello Shantanu, Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files at one go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' Regards, Sampada On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh <shant...@nmr.mgh.harvard.edu > wrote: > 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 >
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