flirt is found in the directory $FSL_DIR, where FSL_DIR is the var set when sourcing $FREESURFER_HOME/SetUpFreeSurfer.csh. What is the output displayed after sourcing SetUpFreeSurfer.csh? And what distribution are you using?

What is the mri_convert command line being used?

On Wed, 2006-03-15 at 17:09 -0500, Chunchun Ni wrote:

I installed the freesurfer following exactly as the instructions on the website. When I test it, "recon-all -s bert -all" doesn't work, it runs for a few min. and shows "flirt: Command not found. ERROR: running flirt". When I try to use my own data, convert dicom to mgt, "mri_convert" command shows "can't find dicom". What's the problem with the installation? Any help?

Thanks Chunchun

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