Hi Julia, I'm not certain, but I think you just need to define FREESURFER_HOME source FS again before trying to run tkmedit or qdec. The "pico $FREESURFER_HOME .license" command resulted in "FREESURFER_HOME: Undefined variable.", so that environment variable needs to be set. I think after the sudo command you were then logged in as root and so the previous environment variables were not carried over. -Louis
On Tue, 16 Oct 2012, Julia Nantes wrote:
I have downloaded the FreeSurfer software onto a Mac computer.
I did the setenv/source steps and got this output:
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
Next, I obtained a license and finally got the text to go into a pico .license file after doing this:
[Lisa-Koskis-iMac:~] rsussex% sudo -s Password: [Lisa-Koskis-iMac:~] root# cd /Applications/freesurfer/ [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico $FREESURFER_HOME .license FREESURFER_HOME: Undefined variable. [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico .license [Lisa-Koskis-iMac:/Applications/freesurfer] root# ls ASegStatsLUT.txt SetUpFreeSurfer.sh fsfast AUTHORS Simple_surface_labels2009.txt lib DefectLUT.txt VERSION matlab FreeSurferColorLUT.txt WMParcStatsLUT.txt mni FreeSurferEnv.csh average sessions FreeSurferEnv.sh bin subjects LICENSE build-stamp.txt tkmeditParcColorsCMA NOTICE data tktools README diffusion trctrain SegmentNoLUT.txt docs SetUpFreeSurfer.csh fsafd [Lisa-Koskis-iMac:/Applications/freesurfer] root# cd ../.. [Lisa-Koskis-iMac:/] root# cd /Applications/freesurfer//subjects/ [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# ls README bert fsaverage fsaverage4 fsaverage6 rh.EC_average sample-002.mgz V1_average cvs_avg35 fsaverage3 fsaverage5 lh.EC_average sample-001.mgz [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# tkmedit bert orig.mgz tkmedit: Command not found. [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# qdec qdec: Command not found.
Since the 'Testing your FreeSurfer installation" commands from the wiki page are not working, I may not have installed this properly.
Any insights as to how this could be resolved would be much appreciated.
Thank you, Julia
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