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
- 255 0 255
- 116 0 116
- 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 ------------------------------ ------------------------------ ------------ ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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 <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.