Thanx Bruce for quick reply.
you are right, it's surface based file after mri_vol2surf. yeah, tried with following command.
tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov lh.seg.mgh -fthresh
0.01 -fmid 0.3 -fslope 1
On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Vin
it looks like your lh.seg.mgh is a surface-based .mgz not a volume one. Did you try loading it into tksurfer?
cheers Bruce
On Wed, 14 Dec 2011, vin . wrote:
Thank you Doug,
tkregister2 --mov $d/T1.nii.gz --targ $d/mri/brain.mgz \
--regheader --reg $d/register.dat --noedit
after creating register.dat, I followed the explained procedure, Which resulted in "lh.seg.mgh". can't view this file. ( appears a line )
mri_info lh.seg.mgh
Volume information for lh.seg.mgh type: MGH dimensions: 163842 x 1 x 1 x 17 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000
mri_info 3b.nii
Volume information for 3b.nii type: nii dimensions: 182 x 218 x 182 voxel sizes: 1.0000, 1.0000, 1.0000
#binary maps looks okay
may be I am doing mistake in registration or mri_vol2surf ?
mri_vol2surf --reg register.dat --mov Nb.nii --interp nearest --hemi lh
--o lh.Nb.mgh
Greetings!
On Tue, Dec 13, 2011 at 5:56 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote: 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 youOn Mon, Dec 12, 2011 at 11:11 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 fromall 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 areoverlaid by atleast half of the subjects ??
>tksurfer #Sub_ID lh inflated -annot aparc.annot -ov1.nii -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1
- How I can overlay multiple regions, in specificcolours, with 50% thr. ? , Thank you :) Vin -----------------------------**-
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