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<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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>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>> >
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>>
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>> >
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>>
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>> >
>>
>>
>>
>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 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>
>
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