[pymvpa] Loading multiple ROIs with fmri_dataset
Lyam.Bailey at Dal.Ca
Wed Aug 14 17:52:15 BST 2019
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.
Lyam Bailey, B.Sc., M.Sc.
Department of Psychology & Neuroscience
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
> 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
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
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
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