[pymvpa] Hemodynamic lag shift

Michael Hanke michael.hanke at gmail.com
Wed Apr 29 17:39:28 UTC 2009


Hi,

On Wed, Apr 29, 2009 at 07:14:25PM +0200, Vadim Axel wrote:
> Thanks. I will use second one.
> 
> With regard ERNiftiDataset: does this class may somehow help to analyze the
> ER designs (specifically fast ER), where the data is extremely contaminated
> with previous BOLD signal?

Yes, that is precisely what it was made for!

But this is pretty new code, don't expect too much.

Michael



> 2009/4/29 Yaroslav Halchenko <debian at onerussian.com>
> 
> > there are a few options you have...
> >
> > in a block design experiment you can either
> > 1. discard volumes on the boundaries of the blocks -- look at
> > idsonboundaries
> > method of a dataset to figure out which volumes you need to discard
> >
> > 2. shift labels to account for  the hemodynamic response... lets say
> > with TR=2 and desired shift of 6 seconds, just shift labels by 3 and
> > discard first 3 volumes... smth like (just typed in... not tested ;))
> >
> > dataset.labels[3:] = dataset.labels[:-3]
> > dataset = dataset.selectSamples(range(3, dataset.nsamples))
> >
> > 3. use BoxcarMapper mapper to just get a mean activation pattern of the
> > block (or simply use that ERNiftiDataset in the fashion similar to
> > ER-dataset analysis)
> >
> >
> >
> > On Wed, 29 Apr 2009, Vadim Axel wrote:
> >
> > >    Hi guys,
> > >    I wonder whether you are making hemodynamic lag shift in pyMVPA? Here
> > >    it the thread, where you discussed this issue with regard to Haxby's
> > >    dataset.
> > >    [1]
> > http://www.mail-archive.com/pkg-exppsy-pymvpa@lists.alioth.debian.or
> > >    g/msg00173.html
> > >    I think it's a critical procedure, especially when designed consists
> > of
> > >    short blocks (like 10-15 secs), where you might miss considerable
> > >    amount of information. As far as I remember in Princeton MVPA matlab
> > >    toolbox such a option existed.
> > >    Thaanks,
> > >    Vadim
> >
> > > Ссылки
> >
> > >    1.
> > http://www.mail-archive.com/pkg-exppsy-pymvpa@lists.alioth.debian.org/msg00173.html
> >
> > > _______________________________________________
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> >
> >
> > --
> > Yaroslav Halchenko
> > Research Assistant, Psychology Department, Rutgers-Newark
> > Student  Ph.D. @ CS Dept. NJIT
> > Office: (973) 353-1412 | FWD: 82823 | Fax: (973) 353-1171
> >        101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102
> > WWW:     http://www.linkedin.com/in/yarik
> >
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> >

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