Hi Bruce & Surfers,

OK, we created a .w file and it looks at is should so part (a) below is solved. However we cannot seem to extract a list of functional overlay values of vertex points included in a label, which was why we needed to do this in the first place.

Our goal is to get rid of some bad vertex points points in our functional overlay by creating a mask that excluded them, then load a label, and use labl_save to create a list of overlay values contained within the label (that does not include the vertex points that were masked away).

Bruce, Kevin, Doug, any suggestions?

Bests,

Tommi

Hi Tommi,

the w-file format is sparse and doesn't have to cover the surface, but the .mgz does.

Bruce

On Tue, 19 Jun 2007 raij@nmr.mgh.harvard.edu wrote:

...

Dear Fellow Surfers,

Is there a FreeSurfer way to mask a stat map overlay, on the inflated cortical surface, in a way that the masked vertex points

(a) are transparent in the overlay display (just the underlying dark gray/light gray curvature is showing)?

(b) do not effect label-specific HDR time courses (i.e., only unmasked vertex points are taken into account when calculating the HDR curve)?

We can edit the stats map with our custom script to generate the mask (e.g., mark all masked vertex points as 0 in the overlay), but it seems that in a stats map every vertex point needs to have an overlay value (i.e., we cannot just skip the vertex points we want to omit - right?).

Thanks!

-Tommi

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Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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