Hi Michael,<br><br>I have the Event definitions stored in a dict (here ev) and read in through a loop like this<br> evt = []<br> for item in ev:<br> # {'onset':runnum*runlength+timestamp,'duration':6,'chunk':runnum,'label':cats[c]}<br>
evt += [Event(onset=item['onset'],duration=item['duration'],chunk=item['chunk'],label=item['label'])]<br><br>Then define the ERNiftiDataset<br><br>data = ERNiftiDataset(samples=dfile,<br>
events = evt,<br> mask=mfile,<br> dtype=N.float32,<br> evconv=True)<br><br>Then the analysis is run with<br><br> smap = LinearNuSVMC().getSensitivityAnalyzer(transformer=N.abs)<br>
results = smap(data)<br><br>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?<br>
<br>Thanks as always,<br>Matt<br><br><div class="gmail_quote">On Thu, Jul 2, 2009 at 7:05 AM, <span dir="ltr"><<a href="mailto:pkg-exppsy-pymvpa-request@lists.alioth.debian.org">pkg-exppsy-pymvpa-request@lists.alioth.debian.org</a>></span> wrote:<br>
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Today's Topics:<br>
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1. ERNiftiDataset (Matthew Cieslak)<br>
2. Re: ERNiftiDataset (Michael Hanke)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 1 Jul 2009 11:59:26 -0400<br>
From: Matthew Cieslak <<a href="mailto:mattcieslak@gmail.com">mattcieslak@gmail.com</a>><br>
Subject: [pymvpa] ERNiftiDataset<br>
To: <a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br>
Message-ID:<br>
<<a href="mailto:83dca85f0907010859y1785fc9dsb4e18fe009531a6a@mail.gmail.com">83dca85f0907010859y1785fc9dsb4e18fe009531a6a@mail.gmail.com</a>><br>
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Hi,<br>
<br>
I just switched from using the transformWithBoxcar function in conjunction<br>
with fsl evfiles to make big files of concatenated samples with labels and<br>
chunks specified in an outside text file to using the ERNiftiDataset class<br>
(which is really nice!) with lists of Event objects and am having trouble<br>
running a searchlight on it. I get the error<br>
<br>
ValueError: Searchlight only works with MappedDatasets that has metric<br>
assigned.<br>
<br>
Is it not possible to use a searchlight when samples have multiple time<br>
points? I had no trouble getting svm weights for the same ERNiftiDatasets,<br>
so I am a little confused<br>
<br>
Thanks,<br>
Matt<br>
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Message: 2<br>
Date: Wed, 1 Jul 2009 18:43:32 +0200<br>
From: Michael Hanke <<a href="mailto:michael.hanke@gmail.com">michael.hanke@gmail.com</a>><br>
Subject: Re: [pymvpa] ERNiftiDataset<br>
To: <a href="mailto:pkg-exppsy-pymvpa@lists.alioth.debian.org">pkg-exppsy-pymvpa@lists.alioth.debian.org</a><br>
Message-ID: <20090701164332.GB10915@runkel><br>
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<br>
Hi Matthew,<br>
<br>
On Wed, Jul 01, 2009 at 11:59:26AM -0400, Matthew Cieslak wrote:<br>
> Hi,<br>
><br>
> I just switched from using the transformWithBoxcar function in conjunction<br>
> with fsl evfiles to make big files of concatenated samples with labels and<br>
> chunks specified in an outside text file to using the ERNiftiDataset class<br>
> (which is really nice!) with lists of Event objects and am having trouble<br>
> running a searchlight on it. I get the error<br>
><br>
> ValueError: Searchlight only works with MappedDatasets that has metric<br>
> assigned.<br>
><br>
> Is it not possible to use a searchlight when samples have multiple time<br>
> points? I had no trouble getting svm weights for the same ERNiftiDatasets,<br>
> so I am a little confused<br>
<br>
Depending on the exact way you are using this dataset type you might<br>
actually get two datasets in one -- one of those has no metric assigned,<br>
because it is not fMRI data. To be able to figure out what is going on<br>
it would be good if you could post the relevant code snippets and an<br>
example of your event definitions.<br>
<br>
Thanks,<br>
Michael<br>
<br>
<br>
--<br>
GPG key: 1024D/3144BE0F Michael Hanke<br>
<a href="http://apsy.gse.uni-magdeburg.de/hanke" target="_blank">http://apsy.gse.uni-magdeburg.de/hanke</a><br>
ICQ: 48230050<br>
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End of Pkg-ExpPsy-PyMVPA Digest, Vol 17, Issue 2<br>
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