It's a little involved but possible.
1. Binarize Nth cluster to have a binary value of N
mri_binarize --i N.nii --min 0.5 --binval N --o Nb.nii
2. Sample Nth cluster to the surface
mri_vol2surf --reg register.dat --mov Nb.nii --interp nearest
--hemi lh lh.Nb.mgh
After doing that will all clusters, combine them together with
mri_concat lh.1b.mgh lh.2b.mgh ... --vote --o lh.seg.mgh
Now create a surface annotation
mris_seg2annot --seg lh.seg.mgh --hemi lh --s subject --o
lh.seg.annot --ctab yourctab
yourctab is a color table like $FREESURFER_HOME/FreeSurferColorLUT.txt.
You list your regions and give them the colors you want.
doug
vin . wrote:
> Hi Doug,
> sorry for confusing names.
>
> - 1.nii is name of the cluster, which I want to overlay. it's a
> coritical region, resulted from fsl-probtrackx.
> I want to have few color codes in RGB
> R G B
> 1. 255 0 255
> 2. 116 0 116
> 3. 0 0 255
> ...
>
> in this way, I would like to overlay 20 cortical regions in different
> colours on inflated brain.
>
> -fthresh 0.3
> here
> (1/(10^0.3) == 50.12 %
> in freesurfer email archieve, I found this. hope it's correct.
>
> Thank you
>
>
>
>
> On Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Vin, why do you say it's a 50% threshold? What is the 1.nii
> data? What colors do you want?
> doug
>
> vin . wrote:
>
> Dear FreeSurfer list,
> Greetings!
>
> a newbie to freesurfer.
> -- would like to overlay tracking group results (Sum from all
> subjects)-(from FSL ) in the inflated lh & rh. --
>
> - it works with one region (hope it's correct), with
> following command, where, -fthresh ?? means it shows 50 %
> threshold based on intensity / only voxels which are overlaid
> by atleast half of the subjects ??
>
> >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov 1.nii
> -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1
>
> - How I can overlay multiple regions, in specific colours,
> with 50% thr. ? ,
> Thank you :)
> Vin
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> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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