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