| Multivariate Pattern Analysis in Python

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This content refers to the previous stable release of PyMVPA. Please visit www.pymvpa.org for the most recent version of PyMVPA and its documentation.

# Spatio-temporal Analysis of event-related fMRI data

The purpose of this example is to show how to use spatio-temporal samples in an event-related fMRI data analysis. We start as usual by loading the PyMVPA suite. The tiny fMRI dataset, included in the sources will server as an example dataset. Although the original paradigm of this dataset is a block-design experiment, we’ll analyze it in an event-related fashion, where each block will be considered as an individual event.

    from mvpa.suite import *

    # filename of the source fMRI timeseries image
    fmri_src = os.path.join(pymvpa_dataroot, 'bold.nii.gz')

    mask = NiftiImage(os.path.join(pymvpa_dataroot, 'mask.nii.gz'))

    # load the samples attributes as usual and preserve the
    # literal labels
    attr = SampleAttributes(
                    os.path.join(pymvpa_dataroot,
                                 'attributes_literal.txt'),
                            literallabels=True)

For an event-related analysis most of the processing is done on data samples that are somehow derived from a set of events. The rest of the data could be considered irrelevant. However, some e.g. preprocessing is only meaningful when performed on the full timeseries and not the segmented event samples. An example is the detrending that typically needs to be done on the original, continuous timeseries. Therefore we are going to load the data twice: first as a simple volume-based dataset for an initial preprocessing, and second to extract the events of interest.

    verbose(1, "Load data for preprocessing")
    pre_ds = NiftiImage(fmri_src)

    # actual labels are not important here, could be 'labels=1'
    pre_ds = NiftiDataset(samples=fmri_src, labels=attr.labels,
                          chunks=attr.chunks, mask=mask)

    # convert to floats
    pre_ds.setSamplesDType('float')

    # detrend on full timeseries
    detrend(pre_ds, perchunk=True, model='linear')

After the detrending, we can now segment the timeseries into a set of events. To achieve this we have to compile a list of event definitions first. In this example we will simply convert the block-design setup defined by the samples attributes into events, so that each block become an event with an associated onset and duration. The necessary chunk settings are taken from these attributes as well. Finally, we are only interested in face or house blocks.

    evs = [ev for ev in attr.toEvents()
                if ev['label'] in ['face', 'house']]

Since we might want to take a look at the sensitivity profile ranging from just before until a little after each block, we are slightly moving the event onsets (one volume prior the actual event) and request to extract a set of twelve consecutive volume a as sample for each event.

    for ev in evs:
        ev['onset'] -= 1
        ev['duration'] = 12

A `ERNiftiDataset` can now be used to segment the timeseries and automatically extract boxcar-shaped multi-volume samples. It is also capable of applying a volume mask.

    # could use evconv...
    verbose(1, "Segmenting timeseries into events")
    ds = ERNiftiDataset(samples=pre_ds.map2Nifti(),
                        events=evs,
                        mask=mask,
                        labels_map={'face': 1,
                                    'house': 2})

For demonstration purposes we copy the pristine dataset before any further processing is done.

    # preserve
    orig_ds = deepcopy(ds)

The rest is pretty much standard. A dataset with spatio-temporal fMRI samples behaves just as any other dataset type. We perform normalization by Z-scoring the data and settle on a linear SVM classifier to perform a cross-validated sensitivity analysis.

    # using rest as baseline
    zscore(ds, perchunk=True)

    clf = LinearCSVMC()
    sclf = SplitClassifier(clf, NFoldSplitter(),
           enable_states=['confusion', 'training_confusion'])

    # Compute sensitivity, which in turn trains the sclf
    sensitivities = \
        sclf.getSensitivityAnalyzer(combiner=None,
                                    slave_combiner=None)(ds)

Before looking at the sensitivity profile we first have to inspect the classifier performance in the cross-validation, since only for a model with reasonable generalization performance it would make sense to interpret the model parameters, i.e. classifier weights. If this is done we could dump the spatio-temporal sensitivity profile, which covers all voxels in the dataset for the full duration of the events, into a NIfTI file.

    print sclf.confusion

    #ds.map2Nifti(N.mean(sensitivities, axis=0)).save('fs_sens.nii.gz')

However, we are going to plot it for some target voxel right away, and compare it to the actual signal timecourse prior and after normalization. We can use the dataset’s mapper to convert the sensitivity vector for each CV-fold back into a 4D snippet.

    # reverse map sensitivities -> fold x volumes x Z x Y x X
    smaps = N.array([ds.mapReverse(s) for s in sensitivities])

    # extract sensitivity profile for target voxel ijk(33,10,0)
    v = (0, 3, 15)
    smap = smaps[:,:,v[0],v[1],v[2]]

Now, we plot the orginal signal after initial detrending,

    P.subplot(311)
    P.title('Voxel zyx%s\nblock-onset@1, block-offset@8' % `v`)
    for l in ds.uniquelabels:
        P.plot(
            ds.mapReverse(
                orig_ds.samples[ds.labels==l].mean(axis=0)
                    )[:,v[0],v[1],v[2]])
    P.ylabel('Signal after detrending')
    P.axhline(linestyle='--', color='0.6')

the peristimulus timecourse after Z-scoring,

    P.subplot(312)
    for l in ds.uniquelabels:
        P.plot(
            ds.mapReverse(
                ds.samples[ds.labels==l].mean(axis=0)
                    )[:,v[0],v[1],v[2]])
    P.ylabel('Signal after normalization')
    P.axhline(linestyle='--', color='0.6')

and finally the associated SVM weight profile for each peristimulus timepoint of the voxel.

    P.subplot(313)
    plotErrLine(smap)
    P.ylabel('Sensitivity')
    P.xlabel('Peristimulus volumes')
    P.axhline(linestyle='--', color='0.6')

    if cfg.getboolean('examples', 'interactive', True):
        # show all the cool figures
        P.show()

See also

The full source code of this example is included in the PyMVPA source distribution (doc/examples/eventrelated.py).

### Navigation

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- previous |
- ExpPsy Project |
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