[pymvpa] Pkg-ExpPsy-PyMVPA Digest, Vol 17, Issue 2

[Matthew Cieslak]

Hi Michael,

I have the Event definitions stored in a dict (here ev) and read in through
a loop like this
    evt = []
    for item in ev:
        #
{'onset':runnum*runlength+timestamp,'duration':6,'chunk':runnum,'label':cats[c]}
        evt +=
[Event(onset=item['onset'],duration=item['duration'],chunk=item['chunk'],label=item['label'])]

Then define the ERNiftiDataset

data = ERNiftiDataset(samples=dfile,
                        events = evt,
                        mask=mfile,
                        dtype=N.float32,
                        evconv=True)

Then the analysis is run with

    smap = LinearNuSVMC().getSensitivityAnalyzer(transformer=N.abs)
    results = smap(data)

In this case the TR is 2sec so results contains 3 volumes. I also tried
setting the duration to 12 seconds and got results spanning 6 volumes. I
assumed that the values in these volumes were just the absolute SVM weights
mapped back from array form to their locations in space/time. Is this
correct?

Thanks as always,
Matt

On Thu, Jul 2, 2009 at 7:05 AM, <
pkg-exppsy-pymvpa-request at lists.alioth.debian.org> wrote:

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> Today's Topics:
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>   1. ERNiftiDataset (Matthew Cieslak)
>   2. Re: ERNiftiDataset (Michael Hanke)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 1 Jul 2009 11:59:26 -0400
> From: Matthew Cieslak <mattcieslak at gmail.com>
> Subject: [pymvpa] ERNiftiDataset
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Message-ID:
>        <83dca85f0907010859y1785fc9dsb4e18fe009531a6a at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I just switched from using the transformWithBoxcar function in conjunction
> with fsl evfiles to make big files of concatenated samples with labels and
> chunks specified in an outside text file to using the ERNiftiDataset class
> (which is really nice!) with lists of Event objects and am having trouble
> running a searchlight on it.  I get the error
>
> ValueError: Searchlight only works with MappedDatasets that has metric
> assigned.
>
> Is it not possible to use a searchlight when samples have multiple time
> points? I had no trouble getting svm weights for the same ERNiftiDatasets,
> so I am a little confused
>
> Thanks,
> Matt
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> ------------------------------
>
> Message: 2
> Date: Wed, 1 Jul 2009 18:43:32 +0200
> From: Michael Hanke <michael.hanke at gmail.com>
> Subject: Re: [pymvpa] ERNiftiDataset
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Message-ID: <20090701164332.GB10915 at runkel>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Matthew,
>
> On Wed, Jul 01, 2009 at 11:59:26AM -0400, Matthew Cieslak wrote:
> > Hi,
> >
> > I just switched from using the transformWithBoxcar function in
> conjunction
> > with fsl evfiles to make big files of concatenated samples with labels
> and
> > chunks specified in an outside text file to using the ERNiftiDataset
> class
> > (which is really nice!) with lists of Event objects and am having trouble
> > running a searchlight on it.  I get the error
> >
> > ValueError: Searchlight only works with MappedDatasets that has metric
> > assigned.
> >
> > Is it not possible to use a searchlight when samples have multiple time
> > points? I had no trouble getting svm weights for the same
> ERNiftiDatasets,
> > so I am a little confused
>
> Depending on the exact way you are using this dataset type you might
> actually get two datasets in one -- one of those has no metric assigned,
> because it is not fMRI data. To be able to figure out what is going on
> it would be good if you could post the relevant code snippets and an
> example of your event definitions.
>
> Thanks,
> Michael
>
>
> --
> GPG key:  1024D/3144BE0F Michael Hanke
> http://apsy.gse.uni-magdeburg.de/hanke
> ICQ: 48230050
>
>
>
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> End of Pkg-ExpPsy-PyMVPA Digest, Vol 17, Issue 2
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