Bruce:
Thanks for that instant reply. I must admit that as soon as I hit "send" on my enquiry, my brain thought "wait a minute -- environment variables?!" and I was just trying that out.
Of course, I would never have found the tksurfer-defined ones, so that's a great help. Probably the rest of the bunch would be useful too....
Thanks,
Graham
Hi Graham, Another way is to generate your TCL on the fly, see below for a simple example:
- snip - #!/bin/sh outdir=/usr/people/johannes/scratch/fssubjects/pictures mkdir -p $outdir
cd $SUBJECTS_DIR # put your subjects here for f in CONTROL*; do for hemi in lh rh; do echo "scale_brain 1.05 redraw save_tiff ${outdir}/${f}_thickness_${hemi}.tiff exit" > /tmp/prettypic_$$.tcl tksurfer $f $hemi inflated -overlay $f/surf/${hemi}.thickness -tcl /tmp/prettypic_$$.tcl done done rm /tmp/prettypic_$$.tcl - snap -
Cheers, Johannes
freesurfer@nmr.mgh.harvard.edu
-
Graham Wideman -
Johannes Klein