glad it worked out :) Bruce On Sun, 20 Aug 2017, Martin Kavec wrote:

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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