Actually, it goes beyond visualisation. That works fine using tksurfer; although, while we're at it: I'd like to use a different colormap (say the jet colormap) but don't seem to be able to do so... suggestions?. I'd like to resample the activation maps and do some surface based searchlight analysis.

Cris

On Wed, May 25, 2011 at 4:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Cris,

why not just visualize it in tksurfer instead?

cheers Bruce On Wed, 25 May 2011, Cris Lanting wrote:

...

Dear all,

I'm trying to read a flattened patch (ascii) using matlab but I'm slightly confused: after performing mris_flatten and mris_convert -p rh.patch.flat rh.patch.flat.asc

I get the following file:

#!ascii version of patch ./rh.orig. The 1st index is not a vertex number 12755 25052 -46888 vno=46887 -47.306606  -24.583883  0.000000 -46894 vno=46893 -44.649334  -26.691339  0.000000 ... 94637 48206 48190 46887 94661 48221 48205 46896

And based on the read_patch script (freesurfer_dir/matlab) I'm able to extract the vertices and faces. vertices_flatmap: -47.3066  -24.5839         0 -44.6493  -26.6913         0 -45.1151  -25.9817         0 ... & faces_flatmap  48206       48190       46887  48221       48205       46896  46893       48218       48219 ...

Yet, if I call

Hpa = patch('vertices',vert_flat,'faces',face_flat,...    'EdgeColor',edgecolor,'FaceColor',facecolor);

it comes up with an error: Warning: Values in patch Faces must be in [1 : rows(Vertices)] - not rendering. I suppose this relates to the fact that it is a subset of the actual complete surface and that it therefore does not start with index 1 (but 48206 instead). Any suggestions how to proceed from here? In the end, I'd like to visualise an overlay (saved as .w file) onto the flattened patch instead of on the inflated surface.

Kind regards and thanks in advance, Cris Lanting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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