External Email - Use Caution
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/freesurfer@nmr.mgh.harvard.edu/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. *Q.2*: I also need to extract Anterior Commissure and Posterior Commissure. *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.
Thanks in advance
Safi