Hi Rebecca,
As John said, uploading your volume is the quickest way for us to help,
but here are some additional thoughts/factors:
* For very non-uniform volumes, 3dUniformize may not be enough. You
might need a bigger gun like FSL's FAST
(http://www.fmrib.ox.ac.uk/fsl/fast/index.html), which does better if
you skull-strip with BET first. I have a script named "fsl_bias_corr.sh"
that takes an input Analyze .hdr and runs BET and FAST on it. You may
need to tweak your FIT and BIAS_SMOOTHING_ITERATIONS iterations to
improve your result:
#!/bin/sh
INFNAME=$1
FSLDIR=/usr/local/fsl
FIT=0.10
BIAS_SMOOTHING_ITERATIONS=500
INBASENAME=`echo $INFNAME | sed 's/.hdr$//g'`
BETBASENAME=`echo $INFNAME | sed 's/.hdr$/_bet/g'`
COMMAND="$FSLDIR/bin/bet $INBASENAME $BETBASENAME -f $FIT -g 0"
echo "========="; echo $COMMAND ; echo "========="
$COMMAND
COMMAND="$FSLDIR/bin/fast -t1 -c 3 -n -v5 -l $BIAS_SMOOTHING_ITERATIONS
-or $BETBASENAME.hdr"
echo "========="; echo $COMMAND ; echo "========="
$COMMAND
* After running FAST, you may find the problem disappears. It's likely
failing during eye or hindbrain removal, both of which are rather
brittle parts of the algorithm. Things that make this part break most
often are:
-- rotation off AC-PC line (see AC work-around below, but there are
definitely limits to how far off AC-PC the volume can be)
-- little CSF clearance between ventral occipital cortex and cerebellum
-- blood vessels or optic nerve preventing disconnection from skull
* Besides correcting for gain/bias field, other things that can help
work around this problem are:
-- peak tweaking: sometimes the difference between WMpeak=75 and
WMpeak=76 can be dramatic
-- adjusting the AC position, especially in the Z (axial) dimension
On 12/06/2006 04:48 PM, John Harwell wrote:
Rebecca,
Can you upload your volume to
http://pulvinar.wustl.edu/cgi-bin/upload.cgi and we will see what is
going on. Please let us know when you have uploaded your volume and
the name of the volume file.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Dec 6, 2006, at 2:48 PM, Rebecca Ebitz wrote:
Hi - I'm having a problem segmenting normalized scans.
I've got a very non-uniform volume (macaque, from a 4.7T w/ 0.5 mm
voxels) and have used AFNI's 3dUniformize to correct these issues.
However, when I try to segment the normalized data in CARET, it
either gives me an error (usually that findBiggestObjectWithinMask
failed in some way) or it simply crashes.
I can run a successful segmentation on the non-uniformized volume, it
just requires a great deal of manual correction. I'm doing the same
processing steps for both the normalized and non-uniform volumes.
Anything I should try here? I've tried to run several different
normalizations and all of them cause segmentation to fail.
Please let me know what other information you need from me on this one.
-Rebecca
______________________________
Rebecca A. Ebitz, post-bac IRTA
Laboratory of Brain and Cognition
National Institute of Mental Health
Building 10, Room 4C214
Office: 301.4510.8509
[EMAIL PROTECTED]
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