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

[Gabriel A. Devenyi]

I care about the vertstats values, so option #1 sounds like the better deal.

--
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 3:53 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> 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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