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  • Visualizing surfaces made by FreeSurfer

How do I run tksurfer or tkmedit from the PINC compute cluster's shared filesystem?

  • NOTE: The text in the two following panels may be downloaded from the attachment to this page.
  • ALSO: These script fragments are for use in /bin/tcsh.  If you normally are using bash, you need to temporarily switch to tcsh if you want to copy these lines of code into your shell.

Do something like the following, once, to prepare your Linux or MacOSX tcsh shell:

setenv PROJECT Kids-CLP
source `which FreeSurf05Env.csh` 10656605

setenv SUBJECTS_DIR /nopoulos/freesurfer/NeuroAmyg_MR/FreeSurfer_Subjects
setenv PROJECT Parcellate_2005

For each mrqid and hemisphere, do something like this:

set mrqid=SM_33_2098_2_97
set hemi=rh

cd ${SUBJECTS_DIR}/${PROJECT}_${mrqid}

tksurfer ${PROJECT}_${mrqid}${hemi} white

tkmedit -f ./mri/rawavg.mgz -surface ./surf/${hemi}.pial -aux-surface ./surf/${hemi}.white

The last two lines are alternatives. Each will put you in one of the FreeSurfer GUIs.

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