Correction:
We want to use func_print_timecourse_selection (not labl_save) to output the tables that contain the means across the label (with the bad vertex points excluded by previously done masking). However I think the time course functions are not compatible with the .w file format? Right, Doug?
Then, I guess the question is, how do we mask the bad vertex points out of the time course volumes?
-Tommi ---
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
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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