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/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.

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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