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,
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
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
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
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
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
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.eduwrote:
oh, so you mean you see a line on the surface?
On Wed, 14 Dec 2011, vin
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
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
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
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
11 matches
Mail list logo
