Nick- I knew it had to be something simple. That did the trick. Thanks for your help! -Robert
On 3/9/08 12:27 AM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Robert,
You can try putting mne setup before the freesurfer setup, that is, swap the 'source...' lines in your .bashrc.
Nick
On Sat, 2008-03-08 at 11:19 -0700, Robert Baldwin wrote:
Hello- I had Freesurfer installed correctly on my Intel Mac OS X machine. Everything was working great. I just installed an MSW (MEG) analysis package and also upgraded my Freesurfer install. This has somehow messed up my paths. I am not sure how to fix.
I have the following commands in my .bashrc
export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source /Applications/MNEMEG/mne/setup/mne/mne_setup_analysis_sh
When I start X11 terminal I get the following:
-------- freesurfer-Darwin-tiger-i686-stable-pub-v4.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni
MNE software location set to /Applications/MNEMEG/mne/ MATLAB software location set to /Applications/MNEMEG/mne/matlab
/Applications/MNEMEG/mne//bin/mne added to PATH /sw/bin added to PATH
Note : Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note : FreeSurfer environment is needed to run mne_setup_source_space
trebor: [/opt/msw] trebor $
However, when I try freesurfer commands I get "command not found" such as:
trebor: [/opt/msw] trebor $ tkmedit bash: tkmedit: command not found trebor: [/opt/msw] trebor $
Any assistance getting me back up and running would be appreciated!
Thanks, -Robert
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