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

[Robert D. Vincent]

Hi Gabriel,

So I have a partial solution. It's a new tool that runs after
scan_object_to_volume and creates a new volume that is a nearest-neighbor
assignment of vertex values to the scanned voxels. As of now, it can only
read a "simple" statistics file that consists of a list of floating point
numbers, but getting basic vertstats support shouldn't be a big deal.

I'll send you the details so you can try it out and see if it seems to work.

    -bert

On Thu, Sep 29, 2016 at 4:07 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> 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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