Hi Falk,
On May 28, 2009, at 3:50 AM, freesurfer-requ...@nmr.mgh.harvard.edu
wrote:
Message: 4
Date: Thu, 28 May 2009 11:56:51 +0200
From: Falk L?sebrink <falk.lu...@gmx.net>
Subject: [Freesurfer] Troubleshooting
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <001501c9df7a$9fe15a40$dfa40e...@luese@gmx.net>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
Im having trouble to generate a correct aseg.mgz for one volume of
mine.
The nu_noneck.mgz is also incorrect and therefore I think the -careg
stage
of autorecon2 might fail. Is there a way to do some kind quality
check, like
the tal-check during autorecon1, to see whether the talairach.m3z is
incorrect? Are there some kind of instructions like fixing the bad
output
from the talairach registration? Or are there some parameters which
can be
adjusted to get better results?
If none of this is possible in some way, would it be advisable to
use the
-noaseg flag? Im actually in no need for the subcortical
segmentation, it
would just be a plus, but the aseg.mgz is needed during the -
segmentation
stage to remove the cerebellum and brain stem. Maybe there even is
another
way to remove these structures automatically?
Well, I can offer a very rough method that seems to work with my
monkey data (where I always use -noaseg), I never tried it with
humans. I edit the wm.mgz and delete two slices worth of midbrain
above the upper connection of the cerebellum to the midbrain. It seems
important that there are no connections from cerebellum left to white
matter (if there are connection above the cut I always delete the
cerebellar part of those, but I do not care about the cerebellum
currently). Then I pick a point on the pons in the segment above the
cut. I use this point, as well as a point picked somewhere in the
middle of the corpus callosum to feed into further recon-all steps
(see below). This probably is rather unclean, but it seems to work
okay, at least with monkey data...
Here my actual script for that step (replace the values in CC_string
and PONS_string with your real values picked from tkmedit of wm.mgz):
# set the target directory and file_name
set targ_dir = ../mri
set src_vol = wm.mgz
#set brain = brain.mgz
set targ_vol = filled.mgz
set controlpoints = ../tmp/control.dat
set cur_dir = `pwd`
# ATTENTION please specify the cutting planes for the pons and the
corpus callosum
# define the raw voxel coordinates for CC and PONS
set CC_string = "128 110 132"
set PONS_string = "128 136 125"#"127 129 112"
# do an initial filling to check the cutting planes
set check_filling = 0
cd ..
set tmp_subj = 0?????*
cd ${cur_dir}
if (${check_filling} == 1) then
echo "Testing the CC and Pons coordinates, if the filled volume
is okay rerun this script with set check_filling = 0"
#mri_fill -CV 127 128 128 -PV 127 154 128 ${src_dir}/${src_vol} $
{targ_dir}/${targ_vol}
mri_fill -a ../scripts/ponscc.cut.log -PV ${PONS_string} -CV $
{CC_string} ${src_dir}/wm.mgz ${src_dir}/filled.mgz
# check the results, left and right white matter should be
colored differently and the cerebellum should be excluded
tkmedit -f ${src_dir}/filled.mgz -aux ${src_dir}/T1.mgz
exit 0
endif
# 20060224
recon-all -autorecon2-wm \
-subjid ${tmp_subj} \
-cc-crs ${CC_string} \
-pons-crs ${PONS_string} \
-noaseg \
-xopts-use
Thanks in advance,
Regards,
Falk
I hope this helps
Sebastian
--
Sebastian Moeller
telephone: 626-395-6713
German GSM: 0 15 77 - 1 90 31 41
moel...@caltech.edu
Division of Biology
MC 114-96
California Institute of Technology
1200 East California Boulevard
CA 91125, Pasadena
USA
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