sorry try:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz Hth, shantanu On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > You don't need the quotation marks in your path > also, it seems you don't have a directory called > /Users/sampada/Desktop/test/org > > try something like: > > cd Users/sampada/Desktop/ > mkdir test > cd test > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > sampada/Desktop/test/s400a1001.nii > > Hth, > shantanu > > > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: >> 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 >>> >> _______________________________________________ >> 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 > > -- 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
