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