AFNI Message Board

History of AFNI updates  

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April 16, 2022 01:14AM
Hi Paul,

I think I know what happened.

I did not split the file, it had been split by ARM/NMT creators. The split versions are registered with AFNI as single-subbrick "ARM Level x" atlases, along with the full 6-subbrick "ARM". Probably to facilitate subbrick selection which - as we have found out - does not seem to work in standard way with whereami.

But here is the actual reason which, as Daniel suggested, was caused by resampling.

NMT2.1 and ARM come in three versions which differ in resolution and/or FOV. The version that registers with afni by running a script provided with NMT/ARM and is consequently used by whereami, is different from the one I was using as the basis of the alignment and then as the atlas. The script registers the large-FOV/0.25 mm version while I am using the tight-FOV/0.5 mm version.

So "my" whereami was resampling my cluster to match the high-res/large FOV version, while the Matlab script directly used the low-res/tight FOV version, also the version whose grid had been imposed on the data. My step-by-step process also explicitly used the low-res version. And you probably registered the 0.5 mm version that I sent you with your AFNI, and your whereami was using it.

Thank you for your help and patience! The good news is that my Matlab script is accurate - ensuring that was the only reason why I compared it to whereami. I will have to use it instead of whereami because I need the percentages of atlas ROIs intersecting with my ROIs, not the other way around.
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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