Hi Simon,
As Donna suggested, there is indeed an option in Connectome Workbench (see
below). In general, we encourage users to convert to Workbench unless their
applications specifically require features only in Caret. Workbench is still
in active development and has many capabilities not available in Caret.
In both cases, it requires that your parcellation be mapped to a cortical
surface, which wasn’t clear from your post.
David
DRAW BORDERS AROUND LABELS
wb_command -label-to-border
<surface> - the surface to use for neighbor information
<label-in> - the input label file
<border-out> - output - the output border file
[-placement] - set how far along the edge border points are drawn
<fraction> - fraction along edge from inside vertex (default 0.33)
[-column] - select a single column
<column> - the column number or name
For each label, finds all edges on the mesh that cross the boundary of
the label, and draws borders through them. By default, this is done on
all columns in the input file, using the map name as the class name for
the border.
> On Feb 7, 2016, at 1:55 PM, Donna Dierker <donna.dier...@sbcglobal.net> wrote:
>
> Hi Simon,
>
> If you can represent your parcellation in Caret paint format, then you can do
> Surface: Region of Interest. There is a feature in there that generates
> areal borders from parcels. The paint format is defined here:
>
> http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#paintFile
>
> You can save the borders as borderproj or border. There are advantages to
> each. Borderproj depends on a particular topology, but you can display the
> borders on the midthickness, inflated, sphere -- any configuration. Border
> depends more on geometry, but can be displayed on multiple meshes (e.g., if
> you fix a topological error, and thus change the number of vertices, you can
> still display the border on both surfaces (before and after patching).
>
> Caret isn't handy right now, so I can't double-check, but it's possible the
> feature that draws borders around clusters requires the vertices to be
> selected, one group/label at a time. If so, you might be able to use
> caret_command to loop through the paint names, selecting each parcel at a
> time, drawing a border around it:
>
> caret_command -surface-region-of-interest-selection
> caret_command -surface-border-draw-around-roi
>
> Then you can open all of the resulting borders at once and save as a
> border/borderproj.
>
> Maybe workbench has a streamlined version of this.
>
> Donna
>
>
> On Feb 6, 2016, at 6:15 PM, Simon Davis <simonwda...@gmail.com> wrote:
>
>> Apologies if this has been addressed previously, but I'm looking to create a
>> border file from a whole-brain set of ROIs (e.g., a novel Craddock
>> parcellation). Any pointers?
>>
>>
>> --
>> Simon W Davis
>> Assistant Professor,
>> Department of Neurology
>> Duke University
>> simon.da...@duke.edu
>>
>> _______________________________________________
>> caret-users mailing list
>> caret-users@brainvis.wustl.edu
>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
>
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