Hi Bryon - I was able to reconstruct the forceps major in your subject
after tweaking some of the 7 control points for the initialization. I'm
attaching the text file with the corrected control points - just drop it
in dlabel/diff and rerun the path reconstruction (don't use reinit,
though!)
I'd definitely not go below 7 control points for this subject b/c of how
convoluted the shape of the forceps major is (due to enlarged ventricles &
thin corpus callosum). You might've even gotten it to work automatically
if you'd gone to more than 7 control points but I haven't tried.
I'll try to incorporate some of this logic into the program in the next
version but if you need to do this edit on more cases in the meantime:
1. Fit a spline to your control points:
dmri_spline --cpts dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt \
--mask dmri/dtifit_FA.nii.gz \
--out dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.nii.gz
2. Display dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.nii.gz on top of
dmri/dtifit_FA.nii.gz and see where the spline strays off the white
matter.
3. Edit dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt by changing one of
the control points that are near the part that's off the white matter.
4. Repeat.
Sorry, this is so not user friendly but we're working on improvements!
Hope this helps a bit,
a.y
On Thu, 29 Nov 2012, bryon mueller wrote:
After processing dozens of subjects through tracula I have found some subjects
with tracts
that are one voxel along the entire tract, for example the forceps major. After
reviewing the
data I believe the bvecs files are pointing the correct direction, I believe
the registration
between the T1/freesurfer segmentation and DTI is reasonably good (registration
was performed
with bbr), at least the anat_brain_mask-vent.bbr and dtifit_FA are reasonable
and cortex.bbr
and lowb_brain seem reasonably well registered. The brain extraction does look
poor in that a
large chunk of posterior skull remains in the anat_brain_mask-vent.bbr image
but the as the
registrations, segmentations and parcellations look OK I believe this isn't the
cause of my
problems.
I do see one issue: the registration between the dtifit_FA.bbr and
fmajor_PP_avg33_mni_bbr_logprior_0 images. Sections of the logprior volume are
entirely in
the lateral ventricles of the DTI data. Please see attached jpg. This subjectÂ
large lateral
ventricles and I am wondering if such subjects can be run successfully in
tracula. Much
thanks for any suggestions.
65.0599 24.5455 29.0648
73.4687 33.3766 22.4575
71.6753 39.7266 24.7112
61.7057 49.7273 27.5844
49.4377 36.6735 27.1492
52.892 30.3552 22.741
57.4436 24.4573 31.4298
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