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

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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