Hi Bruce,
The color LUT would be affected as well. What I mean is that let's say ctx-lh-cuneus has in aparc+aseg.mgz intensity 1005 and I need to give it a custom value. I thought if I could create a file with custom labels and corresponding intensities and give it as parameter to an existing freesurfer binary.
Thanks for inspiration, based on your answer I wrote a short bash script and used fslmaths to remap the values. :)
Best,
Martin
On Sat, Aug 12, 2017 at 10:25 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you mean instead of colors? I guess it would be easy enough to do in matlab. Read in the aseg, use find to find the indices of all the voxels with a particular label, then replace the label with whatever intensity you want.
cheers Bruce On Sat, 12 Aug 2017, Martin Kavec wrote:
Dear all,
I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say,
10
- ventricles, 20 - amygdala, 30 - putamen, ...
I would appreciate advice on how I could achieve that.
Thanks in advance,
Martin
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