THAT was the problem. Thanks so much Bruce. I owe you one. -David
On Sunday, June 3, 2012, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Do you change the vertex indices together 1-based in matlab? I don't see
it...
Bruce
On Jun 3, 2012, at 9:06 PM, David Groppe david.m.groppe@gmail.com wrote:
I. I use read_surf.m to import the pial surface into MATLAB: [cort.vert cort.tri]=read_surf('SUB1/surf/lh.pial');
- I make a completely grey color map for the surface:
map=repmat([1 1 1]*.7,length(cort.vert),1);
- I load the label into MATLAB:
inlabel=read_label('SUB1','res_FINAL');
- I change the color map values of the vertices in the label to red:
map(inlabel(:,1),:)=inlabel([1 0 0],size(inlabel,1),1);
- I plot the surface using tripatch.m
tripatch(cort,1,map);
You can download a MATLAB figure that shows all the vertices of the surface color coded by label (red=label, black=non-label) from here:
http://www.cogsci.ucsd.edu/~dgroppe/label_vertices.fig
If you rotate the figure you can see that some black vertices are
interleaved
in parts of the label area. thanks again, -David
On Sun, Jun 3, 2012 at 5:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
hmmm, and how are you displaying it in the second (patchy) view? I
don't
think tksurfer fills any holes by default
Bruce
On Sun, 3 Jun 2012, David Groppe wrote:
Thanks for the nigh-instantaneous response Bruce. None of the entries have -1 for a vertex number in the first column (see attached). The smallest value is 75. -David
On Sun, Jun 3, 2012 at 5:10 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote:
do any of the label entries have -1 for a vertex number in the first column? If so, tksurfer will sample it onto the surface finding the nearest surface vertex.
On Sun, 3 Jun 2012, David Groppe wrote:
> Hi FreeSurfers, > I am attempting to plot a label in MATLAB using the function > read_label.m. The label was produced in tksurfer (see > label_tksurfer.jpg) from a mask created by FSL. When I try to
import
> the label into MATLAB via read_label.m, I get the correct number of > nonzero vertices (i.e., the same number reported by tksurfer when I > load the label). However the resulting plot is spotty (see > label_matlab.jpg). I suspect that some vertices that are colored as > the label in tksurfer are not actually part of the label file (i.e., > tksurfer is automatically doing some filling in that I'm not aware > of). Is this true? > Any tips on how to solve the problem would be greatly
appreciated.
> much thanks, > -David > >
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