[pymvpa] searchlight for data with different runs with different masks

[Kaustubh Patil]

Hi Yaroslav, thanks for help.

Here is summary for the dataset of one subject:

Dataset: 180x71039 at float64, <sa: chunks,regressors,targets,volumes>, <fa:
voxel_indices>, <a:
add_regs,imgaffine,imghdr,imgtype,mapper,voxel_dim,voxel_eldim>
stats: mean=3.55452e-15 std=1 var=1 min=-4.07657 max=3.95942

Counts of targets in each chunk:
  chunks\targets  0   1
                 --- ---
        1         7   11
        2         16  2
        3         16  2
        4         13  5
        5         9   9
        6         9   9
        7         13  5
        8         15  3
        9         13  5
       10         9   9

Summary for targets across chunks
  targets mean std min max #chunks
    0      12  3.1  7   16    10
    1       6  3.1  2   11    10

Summary for chunks across targets
  chunks mean std min max #targets
    1      9   2   7   11     2
    2      9   7   2   16     2
    3      9   7   2   16     2
    4      9   4   5   13     2
    5      9   0   9   9      2
    6      9   0   9   9      2
    7      9   4   5   13     2
    8      9   6   3   15     2
    9      9   4   5   13     2
   10      9   0   9   9      2
Sequence statistics for 180 entries from set [0, 1]
Counter-balance table for orders up to 2:
Targets/Order  O1     |   O2     |
      0:      119  1  |  118  2  |
      1:       0  59  |   0  58  |
Correlations: min=-0.5 max=0.98 mean=-0.0056 sum(abs)=79




On Sat, Dec 19, 2015 at 11:00 PM, Yaroslav Halchenko <debian at onerussian.com>
wrote:

>
> On Sat, 19 Dec 2015, Kaustubh Patil wrote:
>
> > Thanks a lot Yaroslav. I am following a procedure as described below
> please
> > let  me know if it has any clear or potential problems. I am also
> throwing in
> > another questions here but can start another thread if its worth.
>
> > 1) Alignment procedure: Align all the runs to the middle volume of run1
> > (example_func from fsl). Use the mask that was generated by fsl form
> run1.
>
> ok
>
> > 2) MVPA: do the classifiers give balanced accuracy as my datasets are not
> > balanced?
>
> might need rebalancing.  post output of your dataset.summary() here
>
> > Also, is it recommended to run searchlight on betamap (after fitting
> > hrf) or zscored raw data?
>
> whatever fits your bill.  usually betamaps, and possibly z-scored (per
> run or across all)
>
> > If betamap after fitting hrf then I using the
> > provided function I get only one parameter per target per run, is that
> how its
> > supposed to be?
>
> ok if that is what you want to classify... some times you might
> want model each trial separately.  there is no universal answer.
>
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
>
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