Thank you so much, Bruce.
Yes, I want the CSF inside the brain (e. g. the ventricles). Sorry for being
unspecific.
I see that the way would be to start from filled.mgz and aseg.mgz until I
get the desired ROIs to have the same label (one for white matter, another
for ventricles ) and then run something like mri_mc, right? (Question 1)
Question 2: ok, if this is the way and regarding only white matter surface.
Would there exist significant differences (per hemisphere) between the
surface obtained with mri_mc and the surfaces from recon all? Because
recon-all runs mri_tessellate, mris_smooth, mris_fix_topology
& mris_make_surfaces to obtain the corresponding result... So just mri_mc
does not seem so complete, right?
Q3: I've been trying one example: I have a binary mask with a grid of
101x101x101, 1mm^3 pixel size with the union of two spheres in nifti format.
I run 'mri_mc mask.nii 1 out' and I get a very nice result, but I see
problems regarding orientation. I attach a snapshot of freeview showing this
and also the output of mri_info mask.nii.
Thanks again
Best regards,
Oscar Esteban
Inline image 1
mri_info mask.nii:
Volume information for roi_csf.nii
type: nii
dimensions: 101 x 101 x 101
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 101.000
dof: 0
xstart: -50.5, xend: 50.5
ystart: -50.5, yend: 50.5
zstart: -50.5, zend: 50.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
50.5000
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a =
50.5000
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s =
50.5000
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
1.0000 0.0000 0.0000 0.0000
0.0000 1.0000 0.0000 0.0000
0.0000 0.0000 1.0000 0.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
1.0000 -0.0000 -0.0000 -0.0000
-0.0000 1.0000 -0.0000 -0.0000
-0.0000 -0.0000 1.0000 -0.0000
0.0000 0.0000 0.0000 1.0000
On Tue, Jun 4, 2013 at 3:08 PM, Bruce Fischl <[email protected]>
wrote:
Hi Oscar
what do you mean by "the CSF surface"? Outside the brain or in
the ventricles? If outside, there is some code for creating
boundary element models for EEG/MEG analysis.
There is no trivial way to create a single surface. The way I've
done it in the past is to replace the lh or rh values in the
filled.mgz with the other one and go from there, but it's not
meant to work that way and you have to mess with it a fair
amount.
cheers
Bruce
On Tue, 4 Jun 2013, Oscar Esteban wrote:
Dear all,
I need to extract three surfaces from MRI data:
- GM-WM interface -> thus, lh.white and rh.white
would be the answer.
- Pial interface -> thus, lh.pial + rh.pial
- CSF surface
For CSF, as far as I know, the best option would be
to generate a binary volume merging the appropriate
labels
from aseg.mgz. Then use mri_mc to obtain the
surface, right?
For white and pial I guess the best option would be
to use the recon-all outcome, but I have two
questions:
* Is there any mean to merge both hemispheres? I've
tried several methods but I get trouble with the
consistency of the cells... the points are
aggregated, but no work is done to merge cells and
remove points.
* What are the differences between the recon-all
outcome (lh.pial,rh.pial,lh.white,rh.white) with
respect
obtaining masks from aseg.mgz and then mri_mc?
Thank you so much
Best regards,
Oscar Esteban
--
Oscar Esteban
PhD Student / Researcher
Biomedical Image Technologies (BIT), UPM
ETSI Telecomunicación Lab. C203, Av. Complutense s/n
- E-28040 Madrid (Spain)
+34 915 495 700 ext.4234
Signal Processing Laboratory (LTS5),
EPFL-STI-IEL-LTS5
ELD 224 (Bâtiment ELD), Station 11, CH-1015
Lausanne, Switzerland
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--
Oscar Esteban
PhD Student / Researcher
Biomedical Image Technologies (BIT), UPM
ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid
(Spain)
+34 915 495 700 ext.4234
Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland
