Hi Danny you need to follow the instructions on our wiki. Start with this:
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall then you can go through tthe getting started tutorial as well cheers Bruce On Fri, 24 Nov 2017, Danny Deng wrote:
Dear FS developers, I wish to transform DICOM format to omgz format. However, we have problem when we tried to do recon-all command. The error is as follow: bash-3.2$ export FREESURFER_HOME=/applications/freesurfer bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni bash-3.2$ sudo recon-all -s 'aaa' -i /Users/Dannydeng/desktop/danny_mri/MR22022/DICOM/IM_0001 Password: FREESURFER_HOME: Undefined variable. bash-3.2$ Thanks. Best Regards,Danny Deng
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