I didn't realise caret_command evaluates caret preferences. That's fixed
it. As a suggestion, wouldn't it be nice if there was a command line
qualifier to override preferences for caret_command?
Thanks again,
Johannes
Donna Hanlon schrieb:
Johannes,
Did this still happen after you changed your File: Preferences to write
out ASCII?
This is something I put in a comment in the script, but forgot to point
out in my message. I had the same problem until John told me to change
my preferences. He thinks it's a bug in the way QT is writing binary
files. Once I changed my preferences to ASCII, it worked fine, but I
had to rerun the script.
Donna
On 02/16/2006 10:57 AM, Johannes Klein wrote:
Hi Donna,
the script is quite helpful, thanks! There's one glitch though:
caret_command's averaging of the two .coord's doesn't work, even
though they are both text. The command completes without an error
message, but the contents of the MIDTHICKNESS output file are
illegible, the usual Caret header is missing. Consequently,
segmentation volumes are not generated. I can average the surfaces in
Caret, convert them to text and then create a segmentation volume
(although it looks pretty ugly, see attached).
So it seems the problem is with caret_command - maybe trying (and
failing) to write out a binary file, even though the input is text?
Johannes
Donna Hanlon schrieb:
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
login pub
password download
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
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