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April 15, 2022 11:01PM
Daniel Glen Wrote:
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> This may have to do with differences in the
> resampling/interpolation to the template. Try
> resampling first with 3dresample to the grid of
> the template and nearest neighbor interpolation.

Hi Daniel,

resampling what to the grid of the template? I _think_ that all my files at this point are on the same grid.(or is there anything more to the grid than the Geometry String, Data Axes Orientation, and Data Axes Tilt?)

I start with a structural T2, which I align to the template. After this point, as far as I can tell, the aligned T2 is on the same grid as the template, which is the same grid as the atlas. (by the way, there is no intermediate T1 anymore, but that's a different story)

Next I mask the T2 (same grid), and then I threshold and clusterize it in GUI, and save cluster maps (same grid).

Then I calculate the overlaps between cluster maps and atlas ROIs, and I tried to do it in three ways: via whereami, using afni programs to isolate "my" and atlas ROIs and find intersections, and with a Matlab script that does the same (after cluster maps are converted to NIfTI via AFNI program, as Matlab easily loads NIfTI).

And whereami gives slightly different results than the other two. I agree that the magnitude of the difference suggests something like a side effect of resampling, but I do not understand what and why would be resampled, if the intersected files are on the same grid. Or - again - I think they are.

I should also say that yesterday Paul asked me offline to provide the files, which I did. So maybe he will be able to figure what's going on.
Subject Author Posted

HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 13, 2022 08:33PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 14, 2022 09:08AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 14, 2022 11:11AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 14, 2022 11:17AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 14, 2022 11:23AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 14, 2022 01:50PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 14, 2022 01:56PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 14, 2022 02:07PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 14, 2022 02:32PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 14, 2022 03:51PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 14, 2022 04:09PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Daniel Glen April 15, 2022 10:19PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 15, 2022 11:01PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 15, 2022 11:50PM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 16, 2022 01:14AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

ptaylor April 16, 2022 07:38AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Pawel April 16, 2022 11:22AM

Re: HEAD/BRIK into Matlab (or how to check ROIs against atlas)

Daniel Glen April 17, 2022 10:43PM



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