[MINC-users] Mapping surface (verstats) data into volume space

[Robert D. Vincent]

What I imagine would be something like this:

1. Input a volume template, a surface, and a vertstats file.

2. Every voxel that intersects the surface would be set to the appropriate
value from the vertstats file (possibly using  nearest neighbor or linear
interpolation).

An alternative would be to take a coloured image and copy the colours into
an RGB volume, if you don't care about the actual vertstats values.

On Thu, Sep 29, 2016 at 3:45 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> If scan_object_to_volume could honour colour (optionally), that would
> probably work well. Thanks bert!
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Thu, Sep 29, 2016 at 3:31 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Gabriel,
> >
> > I don't know of a way to do it, but it would be easy to create. I'll look
> > into it if nobody else comes up with a good suggestion.
> >
> >     -bert
> >
> >
> > On Thu, Sep 29, 2016 at 3:27 PM, Gabriel A. Devenyi <
> > gabriel.devenyi at mcgill.ca> wrote:
> >
> > > Thanks!
> > >
> > > I did indeed try after another reply off-list, sadly,
> > scan_object_to_volume
> > > seems to ignore colours.
> > >
> > > --
> > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > Research Computing Associate
> > > Computational Brain Anatomy Laboratory
> > > Cerebral Imaging Center
> > > Douglas Mental Health University Institute
> > > McGill University
> > > t: 514.761.6131x4781
> > > e: gabriel.devenyi at mcgill.ca
> > >
> > > On Thu, Sep 29, 2016 at 3:23 PM, Mishkin Derakhshan <
> mishkind at gmail.com>
> > > wrote:
> > >
> > > > Have you tried making a colored object and then scanning it to
> volume?
> > > >
> > > > Most .obj files default to having just one color per object, and for
> > good
> > > > reason, this lets you overlay different vertstats data and the like
> on
> > > the
> > > > same object. But you can also create a .obj file where the color is
> > > stored
> > > > per vertex. The program to do this is colour_object and should come
> > with
> > > > the default minc installation.
> > > >
> > > > With some luck, scan_object_to_volume will not ignore the colored
> data.
> > > > worth a shot anyway.
> > > >
> > > > Here is some reference material for .obj files:
> > > > http://www.bic.mni.mcgill.ca/Services/HowToWorkWithObjectFiles
> > > >
> > > > In particular you can see how things are colored here:
> > > > http://www.bic.mni.mcgill.ca/users/david/FAQ/polygons_format.txt
> > > >
> > > >
> > > > On Thu, Sep 29, 2016 at 7:45 AM, Gabriel A. Devenyi <
> > > > gabriel.devenyi at mcgill.ca> wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I’m wondering if anyone knows of a method to map verstats data
> (data
> > > on a
> > > > > MNI object) into volume space.
> > > > >
> > > > > I know I can convert an object into a volume representation with
> > > > > scan_object_to_volume. I’d like to then assign values to those
> voxels
> > > > from
> > > > > a verstats file.
> > > > >
> > > > > Thanks!
> > > > >
> > > > > —
> > > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > > Research Computing Associate
> > > > > Computational Brain Anatomy Laboratory
> > > > > Cerebral Imaging Center
> > > > > Douglas Mental Health University Institute
> > > > > McGill University
> > > > > t: 514.761.6131x4781
> > > > > e: gabriel.devenyi at mcgill.ca
> > > > > ​
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