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April 13, 2022 08:33PM
Hello all,

I have an (NHP) cluster map aligned to NMT, which I would like to cross check against the ARM atlas, to produce a report like:
cluster 1: 90% belongs to atlas area 75, 5% to atlas area 133, 5% to nowhere
cluster 2: 14% belongs to atlas area 22, 86 % to nowhere
and then
atlas area 55: 45% in cluster 1, 55% in cluster 3
atlas area 72: 12% in cluster 1, 88% in no cluster
not necessarily exactly in this form, of course. Atlas area names might be included as well.

Is there an AFNI program that would do that for me, ideally with a lot of control over output format?

Alternatively (preferably?) I thought I could just code it in Matlab. But is there a better way to load HEAD/BRIK into Matlab than converting to nifti with 3dAFNItoNIFTI, followed by niftiread in Matlab? I googled up this: [sscc.nimh.nih.gov] but it seems to be old (possibly outdated?) and the link does not work anyway.

Or, if you have other suggestions how to achieve my goal, I'd be happy to hear them.

Two caveats:
If own coding is needed, I would rather stay in Matlab: I know very little of Python and none of R, and coding anything slightly complex in tcsh is not my favorite way of spending time
My Matlab and my AFNI live on the same computer but in different OSes, so I would prefer to avoid mixing up these two, like calling AFNI programs from Matlab script.
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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