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, p
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.
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 f
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
mailto:fis...@nmr
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 wrote:
> oh, so you mean you see a line on the surface?
>
> On Wed, 14 Dec 2011, vin . wrote:
>
> Thanx Bruc
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
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 wrote:
> Hi Vin
>
> it lo
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
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 informat
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 a
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. --
>
>
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
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