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
