[VoxBo] cognitive conjunction analysis in VoxBo

[Daniel Y Kimberg]

Marina Bedny wrote:
> > have n=2, you can use vbperminfo to do the test in a permutation
> > framework.  Use the -pm option and specify multiple perm cube
> > directories.  vbperminfo will create a distribution of "peak minimum
> > values," a confusing phrase that means for each permutation it finds
> > the minimum value, across all the effects, in each voxel.
>
> Okay, that part is done. The output is in /jet2/mbedny/PolyHom/
> conj_inc_cons_cont.txt
> Where do I go from here? The file contains a cut of values, is this
> the maximum min value across volumes described below?

Yes, I think I'm settled on calling it the "peak minimum."

> > Then it
> > picks out the maximum min value across the volume.  Using that
> > distribution, we can pick a threshold to ensure that X% of the time
> > under the null hypothesis, there will be no voxel that exceeds
> > threshold for all effects.
>
> How do I create the conjunction map you're talking about here? Can I
> simply set the threshold for each contrast as to what is specified in
> the output file of what's above and find the overlap? How do I use
> the vbstatmap & vbmaskmunge to get a final conjunction map?

Yes -- you just need to find voxels that are above threshold for both
contrasts.  So create each stat map using vbstatmap, and create the
combined mask by thresholding and quantizing in vbmaskmunge, something
like:

  vbmaskmunge -t <thresh> -q mymap1.cub -o mask1.cub
  vbmaskmunge -t <thresh> -q mymap2.cub -o mask2.cub
  vbmaskmunge -i mask1.cub mask2.cub -o finalmask.cub

Eyeball the masks in vbview to make sure they look like they're
supposed to, but I think that's the right syntax.

> > Using that
> > distribution, we can pick a threshold to ensure that X% of the time
> > under the null hypothesis, there will be no voxel that exceeds
> > threshold for all effects.
>
> Exceeds threshold for all effects or one or more effects? I thought
> it was the latter?

It needs to exceed threshold for all effects.  The logic of the test
is that you're finding voxels where it's unlikely for all N maps to be
above your threshold if there's no effect in any of them.  Using the
minimum across maps means that you're finding voxels where seeing the
effect in all maps is unlikely.

Since you only have two maps, that's the best you can do.  If you
found a threshold at which only one had to be above threshold, it
would be the peak maximum (instead of peak minimum).  That wouldn't be
a useful test, since you could do better just by doing the two maps
independently, and doing a true conjunction test.

dan