you can look in the stats folder in the recon-all output. Eg,
aseg.stats, wmparc.stats. The ?h.aparc*.stats file are surface-based (so
not in the LUT per se), but you can create segmentation volumes from
them (eg, the aparc+aseg.mgz)
On 5/11/2020 10:56 PM, Safi Ullah . wrote:
External Email - Use Caution
Thank you Doug,
With reference to "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" , is there any detail about
the volumes/segmentation link? I mean which mgz files correspond to
which segmentations? may be you have some documentation for that.
With reference to "Not sure, Eugenio will have to weigh in" please
find the attached log file.
Regards,
Safi
On Tue, May 12, 2020 at 2:22 AM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
On 5/10/2020 12:24 PM, Safi Ullah . wrote:
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.
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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