On Wed, Dec 14, 2011 at 7:54 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Have you tried to change the threshold to see if you see more colors? Don't load it as a segmentation, just look at the overlay.
doug

vin . wrote:

Thank you so much Doug,

you are right, it doesn't match exactly, however there is some match. so, now I am running recon-all T1_1mmMNI.nii, probably it will improve the registration.

-extend to previous email -
just to check, I also summed, all binary files. (attached sum_binarymap.tif : output from tksurfer)
>tksurfer Sub_ID lh inflated -ov sum_binmap.nii -overlay-reg register.dat -fthresh 0.01 -fmid 0.3 -fslope 1

here sum_binmap :
>mri_binarize --i N.nii --min 0.1 --binval N --o Nb.nii
>fscalc 1b.nii add 2b.nii add 3b.nii ... -o sum_binmap.nii
>mris_seg2annot --seg sum_binmap.nii --hemi lh --s vin --o lh.seg.annot --ctab vin_colortable.txt

I just wonder, why I only see one color in sum_binmap overlay.

On Wed, Dec 14, 2011 at 6:01 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

The fsaverage surface does not intersect very well with the MNI
brain (the problem is that the average surface does not have as
deep folds as an individual). You can see what is going on if you
convert your label to fsaverage space with

tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.nii
-overlay-reg register.dat

This will show you the surfaces and the label. If the label does
not intersect the surfaces, at all, then there's not much you can
do. If there is some intersection, then you can run mri_vol2surf
with --projfrac-max -.1 1.1 .1

doug

On 12/13/11 10:53 PM, vin . wrote:

#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 <mailto: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
<mailto: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
<mailto:fischl@nmr.mgh.harvard.edu>> wrote:

oh, so you mean you see a line on the surface?

On Wed, 14 Dec 2011, vin . wrote:

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.edu
<mailto: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
<mailto: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 you

On Mon, Dec 12, 2011 at 11:11 PM,
Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto: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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