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');
>>
>> 2. I make a completely grey color map for the surface:
>> map=repmat([1 1 1]*.7,length(cort.vert),1);
>>
>> 3. I load the label into MATLAB:
>> inlabel=read_label('SUB1','res_FINAL');
>>
>> 4. 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);
>>
>> 5. 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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>>>>>
>>>

--
David Groppe, Ph.D.
Postdoctoral Researcher
North Shore LIJ Health System
New Hyde Park, New York
http://www.cogsci.ucsd.edu/~dgroppe/