[pymvpa] Group analysis - surface searchlight
Mike E. Klein
michael.e.klein at gmail.com
Thu Apr 16 15:55:39 UTC 2015
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
> 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  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 . Not
> in PyMVPA yet, but if you are happy to go into Matlab/Octave world, it is
> provided in CoSMoMVPA  through a monte carlo simulation . There is an
> example script  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.
>  https://github.com/PyMVPA/PyMVPA/pull/285
>  http://www.fmrib.ox.ac.uk/analysis/techrep/tr08ss1/tr08ss1.pdf
>  cosmomvpa.org
>  http://cosmomvpa.org/contents_demo.html#demo-surface-tfce
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