Hi Susie - The initial placement of the control points plays a much bigger
role than the end ROIs. The path being initialized in a bad location would
be more of a problem than the end ROIs being too generous. So I'd check
rh.unc_AS_avg32_mni_bbr_cpts_5.nii.gz before editing the end ROIs. Does
that look like it's better placed on right than the left? I'd also check
if the brain mask (aparc+aseg_mask) is any different in that area on one
side.
Hope this helps,
a.y
On Tue, 9 Jul 2013, Susan Kuo wrote:
Hi Anastasia,
For one of my subjects, I am noticing that the right uncinate fasciculus is
very diffuse and more importantly, erroneously crosses from the frontal to the
temporal lobe. I looked at the original endpoint ROI generated by trac-all
-prior (rh.unc_AS_avg33_mni_bbr_end1.nii.gz) and the dilated endpoint ROI in the
temporal lobe (rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz) and noticed that the
endpoints appeared to cross over into the frontal lobe.
Attached is a snapshot for your perusal. On the left side is a display of the
subject/dmri/dtifit_FA.nii with the
subject/dpath/rh.unc_AS_avg33_mni_bbr/path.pd.nii.gz tract superimposed over.
As you can see, the right unc tract crosses from the frontal to the temporal
lobe. On the right side is a display of the subject/dmri/brain_anat_mni.nii.gz with
the endpoints subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2.nii.gz in
green and subject/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1.nii.gz in blue (the
red dots are control points). As you can see, the blue endpoints bleed over from
the temporal to the frontal lobe.
I tried to eliminate these blue points with fslview and then writing over
rh.unc_AS_avg33_mni_bbr_end1.nii.gz. I performed a similar function manually
editing
rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz to better reflect the boundaries . I
subsequently tried to re-run trac-all -path, and unfortunately, all my tracts
looked much worse.
Do you know if incorrectly placed endpoints impair the path reconstruction?
Do you think you can help me? Any advice you can give would be much
appreciated.
--
Susie Kuo
NIH
Mediocrity knows nothing higher than itself, but talent instantly recognizes
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
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