[pymvpa] Group analysis - surface searchlight

[Mike E. Klein]

Many thanks, once again Nick! The full pipeline now works for me.

On Thu, Apr 16, 2015 at 8:50 AM, Nick Oosterhof <
n.n.oosterhof at googlemail.com> wrote:

>
> On 12 Apr 2015, at 00:53, Mike E. Klein <michaeleklein at gmail.com> wrote:
>
> > I’m trying to run a sample top-level analysis on surface-based
> searchlight data using Nick’s afni_surface_alphasim script. I’ve never
> tried this before, and am getting a ZeroDivisionError (bottom of output).
> […]
> >
> > Here is my bash input/output:
> > […]
> > ++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (May  1 2014) [64-bit]
> > ** FATAL ERROR: Dataset
> /Volumes/deep_thought/fmri/mvpa2/april_analyses/subs/06/suma_surfaces_deoblique/zeroed_soundVrest_NEW-minimal_ico32-128_mh_50vx.niml.dset
> differs in size from first one
>
> Actually the issues turned out to be that a an anatomical surface file had
> to be specified. I’ve modified the code now to throw a more informative
> error message if that case is detected, and sent a PR [1] which will
> probably be merged soon. Also the padding actually had to go to 20483 to
> make it work, and increasing the smoothing bandwidth made it run
> significantly faster. So briefly, the options I added that work were:
>
> -N 20483 --surface_file intermediate_surf.asc -S 1.4
>
> where “-N” indicates the node padding (=(32^2*10+2)*2-1), and “-S” the
> smoothing bandwidth.
>
> Also, you may want to consider Threshold Free Cluster Enhancement [2]. Not
> in PyMVPA yet, but if you are happy to go into Matlab/Octave world, it is
> provided in CoSMoMVPA [3] through a monte carlo simulation [4]. There is an
> example script [5] illustrating its use (from "%% Run Threshold-Free
> Cluster Enhancement (TFCE)” onwards). Note: you would have to pad the nodes
> manually and convert to ASCII format, then use cosmo_surface_dataset to
> load each dataset and cosmo_stack to make it a single dataset.
>
> [1] https://github.com/PyMVPA/PyMVPA/pull/285
> [2] http://www.fmrib.ox.ac.uk/analysis/techrep/tr08ss1/tr08ss1.pdf
> [3] cosmomvpa.org
> [4]
> https://github.com/CoSMoMVPA/CoSMoMVPA/blob/master/mvpa/cosmo_montecarlo_cluster_stat.m
> [5] http://cosmomvpa.org/contents_demo.html#demo-surface-tfce
>
>
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