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.
