[pymvpa] Loading multiple ROIs with fmri_dataset

[Lyam Bailey]

Dear Yaroslav,


Fair enough! Thanks again for the help with the add_fa issue, and pointing me in the right direction vis-a-vis the Haxby dataset. I'll look into that.


Regards

Lyam


---------------------------------------------------------

Lyam Bailey, B.Sc., M.Sc.

Doctoral Student

Department of Psychology & Neuroscience
Dalhousie University


________________________________
From: Yaroslav O Halchenko <yoh at onerussian.com>
Sent: Wednesday, August 14, 2019 1:39:44 PM
To: Lyam Bailey <Lyam.Bailey at Dal.Ca>
Cc: pkg-exppsy-pymvpa at alioth-lists.debian.net <pkg-exppsy-pymvpa at alioth-lists.debian.net>
Subject: Re: [pymvpa] Loading multiple ROIs with fmri_dataset


On Wed, 14 Aug 2019, Lyam Bailey wrote:

>    Dear Yaroslav

>    Woops, that was embarrassing! Thanks for clearing that up. However, I've
>    just spotted another potential problem in my code. I assumed that the
>    experimental design was the same for all runs, because only task001_run001
>    (in the sub001/BOLD directory) has an attributes.txt file indicating the
>    order of stimulus presentations (unless I'm very much mistaken?) None of
>    the other runs contain this file, so I used...

>    targets = SampleAttributes(pjoin('haxby2001, 'sub001',
>    'BOLD','task001_run001', 'attributes.txt'))['targets']

>    for every chunk in ds. However, when examining the data loaded in by
>    load_tutorial_data...

>    print ds.targets[ds.chunks==0]
>    > ['scissors' 'scissors' 'scissors'...
>    print ds.targets[ds.chunks==1]
>    > ['face' 'face' 'face'....

>    SO I was clearly wrong on that front. Is there a way to access information
>    about the experimental design from the other runs? As I mentioned above,
>    only task001_run001 contains the relevant attributes.txt file, so I'm
>    rather at a loss as to where the necessary info might be located.

oh... I would need to go for some archaeological expedition to figure
out exactly why, cannot do ATM.

FWIW -- anyways - this is just a demo dataset.  If you really want to
get/analyze haxby2001 -- it is available from openfmri/openneuro in full
"original" shape as ds000105

If you have datalad, you can

datalad install ///openfmri/ds000105

and then

cd ds000105
git checkout 1.0.0

to get old "openfmri" (not BIDS) layout for the dataset.  Unfortunately
we didn't come up with a convenience layer for BIDS datasets yet within
PyMVPA.

--
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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