Hi Emad - Those missing voxels in the mask in the middle of the corpus
callosum could very well be what's not allowing that tract to be
preconstructed.
The file used to create the brain mask from the freesurfer recon is not
mri/brainmask.mgz, but mri/aparc+aseg.mgz, which is mapped to diffusion
space and dilated a bit. This gives you the final mask, which is in
dlabel/diff/aparc+aseg_mask... You can edit this final mask directly in
diffusion space, and then rerun the trac-all steps that come after -masks.
(The editing tutorial on the wiki is about rerunning recon-all, which you
do not have to do if there is nothing wrong with the freesurfer recon.)
Hope this helps,
a.y
On Tue, 9 Dec 2014, Emad Ahmadi wrote:
Hello FreeSurfers!
I am using TRACULA to reconstruct white matter pathways in a patient
with traumatic brain injury. TRACULA has failed to reconstruct forceps
major, and I’m trying to track down why.
I overlaid the FA map (dmri/dtifit_FA.nii.gz) on top of the masked aparc+aseg
(dlabel/diff/aparc+aseg.flt.nii.gz), and I feel fmajor is partially cut by the
mask. Attached please find a slide deck containing the images.
Now I’m trying to edit the brain mask to include the midline of the brain near
the splenium of corpus callosum in the mask. I have two questions:
1. Is my feeling right? Is this small cut of the midline brain the reason of
fmajor recon failure?
2. In the online editorial for brain mask editing, it’s mentioned how to
“shrink” the brain mask, but I cannot find how to “expand” it. I’d appreciate
any help.
Thank you so much,
Emad
Emad Ahmadi, MD
-----------------------------------------------
Research Fellow
Department of Radiology
Massachusetts General Hospital
Harvard Medical School
25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
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