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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. *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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 dgreve@mgh.harvard.edu wrote:
On 5/10/2020 12:24 PM, Safi Ullah . wrote:
External Email - Use CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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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 <dgreve@mgh.harvard.edu mailto:dgreve@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Safi Ullah .