[FieldTrip] Source Point Count & Atlas Point Count Discrepancy

[Sarah]

Hi Konstantinos,

Thank you for your reply, the article link, and the nice visualization code
suggestions!

I agree with you that one reason for the discrepancy is the lack of some
brain regions being part of the atlas itself. I also agree that the 7.5mm
grid is quite coarse so naturally not many source points can fit within an
anatomical region. However, what I am still uncertain about is when you
mention "the boundary between inside and outside is not well defined."

The discrepancy in grid points, that I notice, becomes apparent when you
compare these two observations:
1) when I plot my sourcemodel's grid positions that are marked as "inside"
and my headmodel, I notice a cloud of grid points that appear outside of
the surface of headmodel (even while being considered as "inside"). In
fact, I also use the cfg.inwardshift option when preparing my sourcemodel
to specify an outward shift (because I use a singleshell model), and so I
believe this also increases the number of sources marked as inside.
2) when I retrieve all the atlas points that correspond to my template grid
and plot those grid points with my headmodel, I notice that the grid points
only appear within the volume of the headmodel (ie the cloud of grid points
at or above the surface of the headmodel is not included within the atlas
points even while being considered as "inside")

My question is that given the atlas only seems to be including grid points
that are within the volume of my headmodel, does this mean that specifying
the outer-shift when preparing my sourcemodel to increase source points
that are marked as "inside" is rendered as not useful? In other words,
would there be no point to specify an inward/outward shift in this case
even though I've learned that it may be helpful/recommended for single
shell models in some cases?

Thanks again,
Sarah

On Wed, Jul 3, 2024 at 5:12 PM Sarah <s83728498 at gmail.com> wrote:

> Hi all,
>
>
> I have a question about mapping source points to atlas ROIs.
>
>
> I have computed my source analysis using FT’s 3D grid of 7.5mm. I have
> also interpolated the FT shipped AAL atlas (ROI_MNI_V4.nii) onto this 7.5mm
> template grid.
>
>
> I have now been mapping only some relevant source points to the atlas to
> determine which ROI they exist in. However, I noticed that many of my
> source points didn’t “exist” within the atlas. In fact, the # of my
> subject’s source points that exist inside/outside are reported as: 6871
> dipoles inside, 6791 dipoles outside brain, whereas I notice the atlas
> interpolated source model only has 3475 points total.
>
>
> I was wondering how to handle this apparent discrepancy (as I assume the
> atlas point count should at least be somewhat closer to the total of source
> points marked as inside the brain).
>
>
> Thanks,
>
> Sarah
>
>
> P.S. I included some of my relevant code below to produce this, but it is
> simply the code of the FT tutorials.
>
>
> Subject Sourcemodel Code:
>
> cfg           = [];
>
> cfg.method    ='basedonmni';
>
> cfg.template  = template_grid;
>
> cfg.nonlinear = 'yes';
>
> cfg.mri       = mri;
>
> cfg.unit      ='mm';
>
> grid          = ft_prepare_sourcemodel(cfg);
>
>
> Interpolate Atlas Code:
>
> cfg = [];
>
> cfg.interpmethod = 'nearest';
>
> cfg.parameter = 'tissue';
>
> sourcemodel2 = ft_sourceinterpolate(cfg, atlas, template_grid);
>
> sourcemodel2 = ft_convert_units(sourcemodel2, 'mm');
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240708/05ad9424/attachment.htm>