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 <gr...@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 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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