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Hello,
I'm interested in locating the MGN and LGN using
segmentationThalamicNuclei, but there is a mismatch between their
location in the discrete segmentation (ThalamicNuclei.v10.T1.mgz) and
the underlying probability maps obtained by setting environment
variable WRITE_POSTERIORS to 1. While the LGN in the segmentation has
many voxels within the corresponding area of maximum probability, many
high-probability voxels are missing from it. For the MGN, the
segmentation volume is restricted to a small number of voxels in the
most lateral/posterior/superior part of the area of max probability, but
most high-probability voxels are absent from the segmentation. Any
reason why this could be happening? Is there anything I can do
(parameters I can change in the script) to fix this?
The defaut Freesurfer segmentation ("thalamus proper") is generally
larger than the segmentation output by segmentThalamicNuclei, except in
the area of the LGN, where the thalamic segmentation extends more
laterally/inferiorly, as if it had been extended in order to include the
LGN (although imperfectly). Unfortunately, this does not seem to be the
case for the MGN (which is my primary area of interest).
To solve the issue, I'm thresholding the posterior probability maps at
p>0.2 for both LGN and MGN and adding these voxels to the discrete
segmentation, but that's not very satisfactory. Actually, it wasn't very
clear to me from the published paper how the discrete segmentation is
obtained from the posterior probability maps and if any cut-off value is
used to decide whether to include any voxel in the final discrete
segmentation?
(Note that I'm using T1-weighted MPRAGE data at a resolution of 0.7 mm
isotropic)
Thanks
Julien
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