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Idil,
From the command line with tksurfer open you can use the labl_set_color
command - label is zero indexed based on the order that they were loaded.
See here for more details:
https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferScriptin
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Yes, that looks ok to me.
Regarding code: this is just a draft, and kind of slow/inefficient, but it
should work:
addpath $FREESURFER_HOME/matlab
BRAINSTEM=MRIread(‘brainstemSsLabels.v10.FSvoxelSpace.mgz’);
ASEG=MRIread(‘aseg.mgz’);;
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Hi Eugenio,
Thank you for your reply. The solution to blend the two segmentation will
work for me.
If you could share the Matlab code that would be great.
Also one other related question i have is related to edits and
brainstem-structures.
1. The f
Hi Levin
if you run mris_info on the surface files it should print out the matrices
that freeview uses to compute a voxel coordinate from a surface vertex
location. They are probably different for the BEM surfaces and the ?h.pial
cheers
Bruce
On Thu, 21 Jun 2018, Levin Kuhlmann wrote:
Hi Eugenio,
Thanks for the response. We noted the segmentHA_T1.sh script but weren’t able
to get it running (perhaps you can let me know how to source the development
version of FS and we can try it out). The segmentSubject.sh script seems to be
something you shared with Heidi last year – we de
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Dear Freesurfer Experts,
I have some experience editing the pial surface with tkmedit. (As in this wiki
page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools )
As I recall, this process can be time consuming, because the regener
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Research Assistant Position
The Buckeye Brain Aging Lab (B-BAL)
Department of Psychology
Ohio State University
Applications are being sought for a full-time research assistant position,
in the Buckeye Brain Aging Lab (B-BAL) directed by Dr. Scot
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Dear Mehul,
Yes, the labels from the Brainstem module overlap with the definition of
ventral-dc in aseg.mgz, since they are based on atlas built with delinations
made with different criteria.
A trick you can use to blend the two segmentations into one
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Dear FS list,
( Apologies for asking my question again which I am still struggling to
resolve and which I tried to clarify and condense below. )
I have pre and post-intervention data for a single group of subjects, and
I'd like to extract the cortica
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Hi Nick,
I believe Doug had a similar problem (atlas not flipping for right hippocampus)
because he mixed versions of FreeSurfer. Your call is definitely a bit weird…
First, you’re running the hippocampal subfields with FS6. And then, you’re
calling
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