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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<gr...@nmr.mgh.harvard.edu <mailto: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>
<mailto: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
----------------------------- -
------------------------------
------------
_____________________________ _
_________________
Freesurfer mailing list
freesur...@nmr.mgh.harvard. edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:freesur...@nmr.mgh. harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
https://mail.nmr.mgh.harvard.
edu/mailman/listinfo/
freesurfer
<https://mail.nmr.mgh. harvard.edu/mailman/listinfo/
freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard. edu
<mailto:gr...@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax:
617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>
Bugs: surfer.nmr.mgh.harvard.edu/
<http://surfer.nmr.mgh.harvard.edu/>
fswiki/BugReporting
<http://surfer.nmr.mgh. harvard.edu/fswiki/ BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
FileDrop: www.nmr.mgh.harvard.edu/
<http://www.nmr.mgh.harvard.edu/>
facility/filedrop/index.html
<http://www.nmr.mgh.harvard. edu/facility/filedrop/index. html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
The information in this e-mail is intended only
for the
person to
whom it is
addressed. If you believe this e-mail was sent to
you in
error and
the e-mail
contains patient information, please contact the
Partners
Compliance HelpLine at
http://www.partners.org/ complianceline
<http://www.partners.org/ complianceline
<http://www.partners.org/complianceline>> . If the
e-mail was
sent
to you in error
but does not contain patient information, please
contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax:
617-726-7422 <tel: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>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
