Hi Bryon - It does look like this individual and the tract atlas are not
in good alignment. The one step that requires good alignment is for
choosing an initial guess for the pathway. If the fmajor from all or most
of the subjects that are included in the tract atlas goes through the
ventriclesi of your subject, it'll be tough to get a good initialization
so reconstruction will fail.
You can try the reinit option but in this case you'd have to try it many
times since pretty much all the atlas samples go through your subject's
ventricles.
The last resort for such a subject is to initialize it manually. If you
upload this example subject for me here I can try to see what can be done:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
In principle, once the initialization is ok, the actual path
reconstruction should work even with poor spatial alignment, since it only
uses information on the neighboring aparc+aseg structures and not on the
spatial location of the path. This'll be a chance to test this hypothesis!
Hope this helps,
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 subject large lateral ventricles and I am wondering if such subjects can
be run successfully in tracula. Much
thanks for any suggestions.
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