You're right, thank you, I was looking through the incorrect data set - My original data set (the one I wrote to right after fmri_dataset), has the following mappers:
In [104]: data[1].a.mapper Out[104]: ChainMapper(nodes=[FlattenMapper(shape=(59, 69, 59), auto_train=True, space='voxel_indices'), StaticFeatureSelection(dshape=(240189,), slicearg=array([False, False, False, ..., False, False, False], dtype=bool))]) However, after this data set, I constructed a sub-data set by just selecting certain samples with the target values I wanted, splitting the datasets accordingly, and then reconcatenating them into a new data set. (I then ran the ZScoreMapper() on this new data set, since I only wanted to Z score the samples I was going to use in the searchlight analysis.) In [105]: data_stack[1].a.mapper Out[105]: ZScoreMapper() Finally, I ran the searchlight analysis which resulted in: In [106]: res[1].a.mapper Out[106]: ZScoreMapper() Would it then be accurate for me to simply use the ChainMapper from the original data set (exclude the ZScoreMapper from the map2nifti function), like so: map2nifti(data[1], res[1].samples) Or would it be more accurate of me to construct a new ChainMapper which includes the ZScoreMapper, append it to the ChainMapper of the original data set, and then re-attribute it to the searchlight output data set? Thanks again! This has been a huge hassle, and you've been a great help (though I realize that much of the troubles were my own carelessness now... Sorry!). Taku On Mon, Nov 4, 2013 at 11:00 AM, Yaroslav Halchenko <[email protected]>wrote: > > On Mon, 04 Nov 2013, Taku Ito wrote: > > > Oh! �I did in fact have one, though it's the Zscore-mapper (I had > > previously thought I checked 'mapper' in res[1].a, but perhaps it > came out > > incorrectly). �Though I realize Z-score mapper probably doesn't have a > > reverse mapper, and perhaps that's the issue? �Is there a workaround > you > > may be aware of? > > hm -- it should not be just a zscore mapper but rather also the ones > which lead to that point. (flattening, feature selection (you had a > mask, right?)). please show print ds.a.mapper and if it is indeed only > zscore -- then a code snippet which lead to that point. Inspect also > either you had a correct mapper right after fmri_dataset > > > Thanks! > > > On Mon, Nov 4, 2013 at 10:48 AM, Yaroslav Halchenko > > <[1][email protected]> wrote: > > > On Mon, 04 Nov 2013, Taku Ito wrote: > > > > � �Are all datasets supposed to have mappers? �My data set was > loaded > > > � �directly from a NIFTI file, using > mvpa2.datasets.mri.fmri_dataset, > > and > > > � �when I loaded it there was no mapper attached, > > > it should be there under .a.mapper ... see e.g. > > [2]http://www.pymvpa.org/tutorial_datasets.html#loading-fmri-data > > for more information > > > though I attributed it > > > � �target values and chunks. �In other words, my original data set > > also does > > > � �not have any mappers. �Should I be manually attributing > mappers to > > my data > > > � �set (e.g., the searchlight call or the z-scoring call) and > attach > > all > > > � �those mappers as a Chain? > > > let's first figure out if you indeed didn't have any ;-) > -- > Yaroslav O. Halchenko, Ph.D. > http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org > Senior Research Associate, Psychological and Brain Sciences Dept. > 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 > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > -- Takuya Ito Cognitive Control & Psychopathology Laboratory Washington University in St. Louis Cole Neuroscience Laboratory (http://www.mwcole.net/) Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers-Newark University
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