#Registration
>tkregister2 --mov $d/T1.nii.gz --targ
$d/mri/brain.mgz \
--regheader --reg $d/vin_register.dat --noedit
I have cortical-clusters in 1mm MNI space so, I took 1mm MNI brain and registered this on the "fsaverage" default subject's /mri/brain.mgz"
Find attached register.dat
#checking registration
>
tkregister2 --targ $d/mri/brain.mgz \
--mov T1.nii.gz --reg vin_register.dat
find attached register.tiff
Regards,
vin
On Wed, Dec 14, 2011 at 4:40 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Is your register.dat correct?
On 12/13/11 10:33 PM, vin . wrote:Thanx Doug,
atleast I see, now something. (see attached "seg.mgh -annot seg.annot.tiff)
> tksurfer Sub_ID lh inflated -annot seg.annot -ov lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1
just to check, I also summed, all binary files. (attached sum_binarymap)
>tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg register.dat -fthresh 0.01 -fmid 0.3 -fslope 1
also find colortable.
Greetings!
On Wed, Dec 14, 2011 at 4:18 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Try tksurfer Sub_ID lh inflated -annot seg.annot
doug
On 12/13/11 9:39 PM, vin . wrote:no, in tksurfer, just inflated lh appears (no overlay). so, I viewed lh.seg.mgh in freeview and converted it to .nii and viewed in fslview.
On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
oh, so you mean you see a line on the surface?
On Wed, 14 Dec 2011, vin . wrote:
$FREESURFER_HOME/ FreeSurferColorLUT.txt. YouThanx 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.edu>
wrote:
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
<http://www.partners.org/ complianceline> . If the
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
<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
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