On 5/10/2020 12:24 PM, Safi Ullah . wrote:
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Dear Freesurfer,
*Q.1*: The colors of FreeSurferColorLUT.txt corresponds to which mgz file?
I wanted to extract Substancia-Nigra but with reference to a
conversion, held in 2019,
https://www.mail-archive.com/[email protected]/msg63560.html,
segmentation for the serial # of Substancia-Nigra is not supported in
version 6, is it supported by Version 7? if not then i would like to
write a code to extract labels for Substancia-Nigra based on the color
code (RGB). is it possible? as the slices are in grayscale.
There is not a single mgz file that has all of those segmentations, and
there are some ROIs that we do not segment yet, substantia nigra being
one of them.
*Q.2*: I also need to extract Anterior Commissure and Posterior
Commissure.
We do not segment AC or PC yet either.
*Q.3*: While reading the brainstem-structures.log, I came across this
statement (it appears multiple times)
" * WARNING: Registration did not converge in 5 steps!
* Problem might be ill posed.
* Please inspect output manually! "
why i get this warning and how to get rid of it? because i think the
segmented midbrain does not cover the whole midbrain area.
Not sure, Eugenio will have to weigh in.
Thanks in advance
Safi
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