Hi caret-users,
This script may be helpful to those who import Freesurfer surfaces into
Caret for various purposes.
http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
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It does the following:
* calls mris_convert to convert the Freesurfer binary surfaces to ASCII
* converts the Freesurfer ASCII surfaces to Caret coord/topo files
* averages the pial and smoothwm surfaces to generate a midthickness coord
* creates a spec file with the hem_flag as left or right
* generates the sulcal depth and geography paint file from the
midthickness surface
Run this script in a 'subjects' directory where there is a subdirectory
for each case/subject. This script assumes there is a surf subdirectory
under each case subdirectory, e.g.:
./ED/surf
./EF/surf
./EG/surf
./FH/surf
./FK/surf
./FL/surf
./FM/surf
./FN/surf
Then, change this line in the script to reflect your actual case/subject
subdirectory names:
CASES="ED EF EG FH FK FL FM FN"
If you have additional layers between the case subdirectory and your
Freesurfer surf subdirectory, then you'll need to tweak these lines
accordingly:
cd $CASE/surf
...
cd ../..
Disclaimers:
1. The origin setting in the caret_command -volume-create step reflects
my best current understanding of where the Freesurfer origin actually
is. Help in clarifying this issue is most welcome. The bottom line is
that the depth measures will be accurate regardless of the actual origin
input here, because the segmentation and derivative hull volume will be
generated from the same origin, so the resulting distance between the
fiducial and hull surfaces will not be affected by the actual origin
setting; however, someone might try to align these derivative volumes
with an actual anatomical generated from the COR-* slices and
midthickness fiducial surface. There may be slight offset issues,
although the alignment looks good to me. More importantly, it would be
nice to add a Freesurfer atlas space for the -volume-create and
paint/metric-to-volume features.
2. I confess I haven't tested it as thoroughly as I'd like to.
Apologies: Sorry I didn't get this up sooner; my daughter was sick
yesterday.
Donna
