Dear mrtrix community,
I would like to use cortical ROIs to reconstruct a tract of interest. In my case, I have mammilary bodies and hippocampus ROI in the goal of reconstructing the fornix. The thing is that the fornix is poorly drawn on the white matter mask from
As a result, reconstruction of the fornix with the mammilary bodies as
seed_image and the hippocampus as an
include image with the
-act option gives no results:
By not using the
-act option in
tckgen (and a lot of exclusion ROIs), I obtain a reconstruction of the fornix. But there are a lot of ‘messy’ streamlines, possibly because of the absence of
To reconstruct the Fornix while using
-act, would it make sense to replace the white matter mask from the
5tt file with a dilated white matter mask? If I dilate the wm mask by 1 voxel, the white matter corresponding to the location of the fornix is visible:
I have read elsewhere on the forum that the use of
connectome2tck on a whole-brain tractogram was advised in the case of cortical ROIs instead of
tck2connectome performs a 2mm radial search to assign streamlines to cortical ROIs.
However I would prefer to use
tckgen with cortical ROIs to reconstruct the fornix as I feel that I have more control on the tracking options (e.g., I set a low max length and a high cutoff value to reconstruct only the wanted streamlines). Obviously, i could set these optimal
tckgen parameters while doing whole-brain tractography with my edited
5ttgen file (containing a dilated white matter mask to allow reconstruction of streamlines at the location of the fornix) and then feed this tractogram to
tck2connectome, but does this make sense?
Would the use of
-act + with a dilated white matter mask + cortical ROIs solve the streamlines assignment problem? Should I dilate my cortical ROIs as well? Or dou you advise using tck2connectome after whole-brain tractography on the dilated white matter mask?