On Tue, 13 Aug 2019, Lyam Bailey wrote: > Dear users,
> I am trying to manually load in the PyMVPA tutorial data, instead of using > the load_tutorial_data convenience function (as shown here, for example: > http://www.pymvpa.org/examples/rsa_fmri.html). I have downloaded the > tutorial data and replaced the following lines of code from the example > script: > from mvpa2.datasets.sources.native import load_tutorial_data > datapath = pjoin(cfg.get('location', 'tutorial data'), 'haxby2001') > ds = load_tutorial_data(roi=(15, 16, 23, 24, 36, 38, 39, 40, 48)) > with the following loop: > data_path = pjoin('haxby2001', 'sub001') > runs = [1,2] > run_datasets = [] > targets = SampleAttributes(pjoin(data_path, 'BOLD','task001_run001', > 'attributes.txt'))['targets'] > for i in runs: > bold_fname = pjoin(data_path, 'BOLD', 'task001_run00' + str(i), > 'bold.nii.gz') > temp_ds = fmri_dataset(bold_fname, mask=None, targets = targets, > chunks = i-1) > run_datasets.append(temp_ds) > ds = vstack(run_datasets, a=0) > The one thing I'm missing is how to load in multiple ROIs, as in ds = > load_tutorial_data(roi=(15, 16, 23, 24, 36, 38, 39, 40, 48)). Is > there a way to achieve this with fmri_dataset? Or is there a more fmri_dataset has an argument: add_fa : dict or None Optional dictionary with additional volumetric data that shall be stored as feature attributes in the dataset. The dictionary key serves as the feature attribute name. Each value might be of any type supported by the 'mask' argument of this function so you could point to any ROI masks/index volumes and get them assigned to a .fa $> python -c 'import mvpa2.suite as mv ; print(mv.fmri_dataset("mvpa2/data/haxby2001/sub001/BOLD/task001_run001/bold_25mm.nii.gz", add_fa={a: "mvpa2/data/haxby2001/sub001/masks/25mm/%s.nii.gz" % a for a in ["brain", "gray", "vt"]}))' <Dataset: 121x600@int16, <sa: time_coords,time_indices>, <fa: brain,gray,voxel_indices,vt>, <a: imgaffine,imghdr,imgtype,mapper,voxel_dim,voxel_eldim>> -- 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 _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
