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

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 <fischl@nmr.mgh.harvard.edu> 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