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
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.