You could also try the nipy version. works real well with Snow Leopard OS shantanu
On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote: > Hi Sampada, > > Please cc the freesurfer list when answering/asking questions so others > can answer too. And also people with similar issues will benefit from the > discussion. > > see inline for my responses. > > Hth, > shantanu > > On Mon, April 28, 2014 8:27 pm, Dr Sampada Sinha wrote: >> Hello Shantanu, >> >> Thanks for your reply.I tried using that as well. And it says that the >> file >> is only 'read' file. I used chmod on unix but still its not working with >> dcm2nii. Interstingly, when I used mriconvert software for this,it >> converted all the dcm files to .img/.hdr files. This process resulted in >> eight folders (in .img/.hdr format) 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). >> Is there any special command you are using to convert those files >> Shantanu? > > You can edit dcm2nii.ini file using any text editor after it is created > automatically (by running dcm2nii for the first time). It operates like a > shell program and can be run from your analysis directory by sourcing it > first. > > If you look at the dcm2nii file you can use custom settings. To get the > output nii as a single file set the SingleNIIFile=1 and 4D=1, otherwise by > default you get the img/hdr pairs > > If further you want nii.gz instead of nii files, use Gzip=1 setting > > If this doesn't work, you could use the Windows version to convert with > the same settings that I describe above. > >> If yes, will you please let me know? Where do you keep your dcm files >> (iyou >> don't mind me asking that)? I tried changing the location from Desktop >> to >> Applications/freesurfer as well, but its still not working. > > The dcm files can be anywhere, you have to source them correctly by > providing the correct path. Or drag/drop into the window if you are using > the gui. > > >> >> Thanks and regards, >> >> Sampada >> >> >> >> On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < >> shant...@nmr.mgh.harvard.edu> wrote: >> >>> You can convert Dicom using MRICroN with the dcm2nii utility >>> >>> shantanu >>> >>> >>> On Mon, April 28, 2014 6:55 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 >>> >>> >>> -- >>> 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 >>> >>> >>> 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. >>> >>> >> > > > -- > 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 > > > -- 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
