However, it appears to be limited to SPM's interactive window for exploring results, and thus to clusters that are defined statistically (and have a corresponding SPM.mat file).
What I would looove to see is a "save current cluster" function in an image viewer that is displaying my binary .nii image of spatially separated clusters. That is, an implementation of something similar what your script does into an interactive image viewer.
Anyway, until someone comes up with that I'll be just fine with the scripts you and Donald provided.
Thanks a lot for that again.
> Date: Wed, 5 Dec 2012 11:06:24 +0100
> From:
[log in to unmask]> To:
[log in to unmask]> CC:
[log in to unmask]> Subject: Re: [SPM] Extract clusters from binary mask
>
> > Would be a great tool for an image viewer: click somewhere into a
> > spatial cluster (not necessarily a stats output) and have it written out
> > as a .nii file.
>
> ... you mean, you would love to see a "save current cluster" function in
> the "save" dropdown field in spm's interactive window when exploring
> results? Well, go check, somebody obviously requested that feature before :)
>
> Cheers,
> Marko
>
>
>
> > > Date: Tue, 27 Nov 2012 11:51:37 -0500
> > > Subject: Re: [SPM] Extract clusters from binary mask
> > > From:
[log in to unmask]> > > To:
[log in to unmask]> > > CC:
[log in to unmask]> > >
> > > My peak_nii toolbox will also provide you with the information you
> > > want. I expect to add a few more features in the coming weeks -
> > > including the center of binary clusters and probability of a cluster
> > > being in a given anatomical region.
> > >
> > > Best Regards, Donald McLaren
> > > =================
> > > D.G. McLaren, Ph.D.
> > > Research Fellow, Department of Neurology, Massachusetts General
> > Hospital and
> > > Harvard Medical School
> > > Postdoctoral Research Fellow, GRECC, Bedford VA
> > > Website: http://www.martinos.org/~mclaren
> > > Office: (773) 406-2464
> > > =====================
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> > >
> > >
> > > On Tue, Nov 27, 2012 at 6:36 AM, Michel Grothe
> > <
[log in to unmask]> wrote:
> > > > Dear SPMers,
> > > >
> > > > does anyone know a simple/automatic way to isolate spatially
> > separate clusters from a binary mask?
> > > > XJview for example allows you to isolate single clusters from
> > T-maps, but it doesn't work in my case of a binary mask.
> > > > Any hints will be highly appreciated.
> > > >
> > > > Best,
> > > > Michel
>
> --
> ____________________________________________________
> PD Dr. med. Marko Wilke
> Facharzt für Kinder- und Jugendmedizin
> Leiter, Experimentelle Pädiatrische Neurobildgebung
> Universitäts-Kinderklinik
> Abt. III (Neuropädiatrie)
>
>
> Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
>
> Hoppe-Seyler-Str. 1
> D - 72076 Tübingen, Germany
> Tel. +49 7071 29-83416
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>
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