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.
