Hi Swann,
With the regular Volume: SureFit Operations (Segmentation), I'm pretty
sure you still need to crop to a left or right hemisphere. So before
launching segmentation, you'd still need to Volume: Resize underlay
volume to crop it. (I say pretty sure, because John Harwell is always
making enhancements, and sometimes I'm surprised to find cool features
by accident.)
Back in May, though, John did add some automatic segmentation features
that looked very promising, based on initial results, but which no one
to my knowledge has tested extensively. Perhaps you can be the person
to do so. ;-)
He had a shell script loop through case directories like so:
pushd ./case01/LEFT_HEM/
run_seg.csh
popd
pushd ./case01/RIGHT_HEM/
run_seg.csh
popd
pushd ./case42/LEFT_HEM/
run_seg.sh
popd
pushd ./case42/RIGHT_HEM/
run_seg.sh
popd
Then in each of these left and right hem subdirs, there was a tiny
script like this:
#!/bin/csh
caret_command -volume-segment-stereo-space \
-ecv \
human.case42.L.spec \
Human_Buckner_Case42+orig.HEAD
This is what the usage says:
THIS IS EXPERIMENTAL BUT IT WILL PRODUCE A SURFACE
The input spec file must contain the stereotaxic space
and the
structure (LEFT or RIGHT) for this command to operate. A
spec
is created by running this program with the
"-spec-file-create"
command.
So, you can either crop manually; run caret_command
-volume-segment-stereo-space on it (crossing your fingers); or simply
use the old Colin surfaces, which are still available in sumsdb.
Why are you segmenting Colin, anyway? There already are several
surface-based versions of it.
Donna
On 11/08/2007 04:45 AM, swann pichon wrote:
Dear all,
I encounter an (out of) memory error during the determination of the
inner boundaries of a 1^3 human T1 (colin27). I launched Surefit onto
the T1 Colin27 (both hemisphere at the same time) available here :
http://imaging.mrc-cbu.cam.ac.uk/downloads/Colin/
I Used the following parameters
o/utput format to NIFTI
gray: 81
white: 105
//
//hindbrain off
/
/Automatic err correction : off
Correct all topological ... off
Generat inlated off
very inflated off
elipsoidal : off
everything else is on
/
I am running winXPsp2, P43.4 GhZ with 2G° RAM & 2000 to 8000M° max of
swap space.
How much RAM is needed to run Surefit in this context ?
Thanks a lot for your comments,
All the best,
Swann
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