예제 #1
0
def runsub(sub, thisContrast, r, dstype='raw', roi='grayMatter', filterLen=49, filterOrd=3, write=False):

    if dstype == 'raw':
        outdir='PyMVPA'
        print "working with raw data"
        thisSub = {sub: subList[sub]}
        dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi)
        thisDS = dsdict[sub]
        mc_params = lmvpa.loadmotionparams(paths, thisSub)
        beta_events = lmvpa.loadevents(paths, thisSub)
        # savitsky golay filtering
        sg.sg_filter(thisDS, filterLen, filterOrd)
        # gallant group zscores before regression.

        # zscore w.r.t. rest trials
        # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
        # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
        zscore(thisDS, chunks_attr='chunks')
        print "beta extraction"
        ## BETA EXTRACTION ##
        rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
        evds = er.fit_event_hrf_model(rds, events, time_attr='time_coords',
                                      condition_attr=('trial_type', 'chunks'),
                                      design_kwargs={'add_regs': mc_params[sub], 'hrf_model': 'canonical'},
                                      return_model=True)

        fds = lmvpa.replacetargets(evds, contrasts, thisContrast)
        fds = fds[fds.targets != '0']
    else:
        outdir=os.path.join('LSS', dstype)
        print "loading betas"
        fds = lmvpa.loadsubbetas(paths, sub, btype=dstype, m=roi)
        fds.sa['targets'] = fds.sa[thisContrast]
        zscore(fds, chunks_attr='chunks')

    fds = lmvpa.sortds(fds)
    print "searchlights"
    ## initialize classifier
    clf = svm.LinearNuSVMC()
    cv = CrossValidation(clf, NFoldPartitioner())
    from mvpa2.measures.searchlight import sphere_searchlight
    cvSL = sphere_searchlight(cv, radius=r)


    # now I have betas per chunk. could just correlate the betas, or correlate the predictions for corresponding runs
    lidx = fds.chunks < fds.sa['chunks'].unique[len(fds.sa['chunks'].unique)/2]
    pidx = fds.chunks >= fds.sa['chunks'].unique[len(fds.sa['chunks'].unique) / 2]

    lres = sl.run_cv_sl(cvSL, fds[lidx].copy(deep=False))
    pres = sl.run_cv_sl(cvSL, fds[pidx].copy(deep=False))

    if write:
        from mvpa2.base import dataset
        map2nifti(fds, dataset.vstack([lres, pres])).\
            to_filename(os.path.join(
                        paths[0], 'Maps', outdir,
                        sub + '_' + roi + '_' + thisContrast + '_cvsl.nii.gz'))

    del lres, pres, cvSL

    cvSL = sphere_searchlight(cv, radius=r)
    crossSet = fds.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cres = sl.run_cv_sl(cvSL, crossSet.copy(deep=False))
    if write:
        map2nifti(fds, cres[0]).to_filename(
            os.path.join(paths[0], 'Maps', outdir,
                         sub + '_' + roi + '_' + (thisContrast) + '_P2L.nii.gz'))
        map2nifti(fds, cres[1]).to_filename(
            os.path.join(paths[0], 'Maps', outdir,
                         sub + '_' + roi + '_' + (thisContrast) + '_L2P.nii.gz'))
예제 #2
0
def runsub(sub, thisContrast, thisContrastStr,
           filterLen, filterOrd,
           paramEst, chunklen, alphas=np.logspace(0, 3, 20), debug=False, write=False, roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    # rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts) # adding features

    # we can model out motion and just not use those betas.
    # Ridge
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    # instead of binarizing each one, make them parametric
    desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
                                     design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
                                     regr_attrs=None)
    # want to collapse ap and cr, but have anim separate
    desX['motion'] = make_dmtx(rds.sa['time_coords'].value, paradigm=None, add_regs=mc_params[sub], drift_model='blank')

    des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)

    # set chunklen and nchunks
    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]
    nchunks = int(len(thisDS)*paramEst / chunklen)
    nboots=50
    covarmat = None
    mus = None
    lwts, lalphas, lres, lceil = bsr.bootstrap_ridge(rds[lidx], ldes, chunklen=chunklen, nchunks=nchunks,
                                              cov0=covarmat, mu0=mus, part_attr='chunks', mode='test',
                                              alphas=alphas, single_alpha=True, normalpha=False,
                                              nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
                                              plot=debug, use_corr=True)

    pwts, palphas, pres, pceil = bsr.bootstrap_ridge(rds[pidx], pdes, chunklen=chunklen, nchunks=nchunks,
                                              part_attr='chunks', mode='test',
                                              alphas=alphas, single_alpha=True, normalpha=False,
                                              nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
                                              plot=debug, use_corr=True)
    print 'language ' + str(np.mean(lres))

    # pictures within
    print 'pictures: ' + str(np.mean(pres))

# need to change outstring
    if write:
        from mvpa2.base import dataset
        map2nifti(thisDS, dataset.vstack([lres, pres])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_corrs.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_weights.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lalphas, palphas])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_alphas.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_ceiling.nii.gz'))

    del lres, pres, lwts, pwts, lalphas, palphas, lceil, pceil
    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cwts, calphas, cres, cceil = bsr.bootstrap_ridge(crossSet, des, chunklen=chunklen, nchunks=nchunks,
                                              part_attr='chunks', mode='test',
                                              alphas=alphas, single_alpha=True, normalpha=False,
                                              nboots=nboots, corrmin=.2, singcutoff=1e-10, joined=None,
                                              use_corr=True)
    print 'cross: ' + str(np.mean(cres))
    if write:
        map2nifti(thisDS, cres[0]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_corr.nii.gz'))
        map2nifti(thisDS, cres[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_corr.nii.gz'))

        map2nifti(thisDS, cwts[0]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_weights.nii.gz'))
        map2nifti(thisDS, cwts[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_weights.nii.gz'))

        map2nifti(thisDS, calphas[calphas.chunks==1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_alphas.nii.gz'))
        map2nifti(thisDS, calphas[calphas.chunks==2]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_alphas.nii.gz'))

        map2nifti(thisDS, cceil[0]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_ridge_ceiling.nii.gz'))
        map2nifti(thisDS, cceil[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_ridge_ceiling.nii.gz'))
    del cres, cwts, calphas, cceil
예제 #3
0
def runsub(sub, thisContrast, thisContrastStr, testContrast,
           filterLen, filterOrd, write=False, debug=False,
           alphas=1, roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts)  # adding features

    # we can model out motion and just not use those betas.
    # Ridge
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
                                     design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
                                     regr_attrs=None)
    # 'add_regs': mc_params[sub]

    desX['motion'] = make_dmtx(rds.sa['time_coords'].value, paradigm=None, add_regs=mc_params[sub], drift_model='blank')

    des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)

    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]

    covarmat = None
    mus = None
    lwts, _, lres, lceil = bsr.bootstrap_ridge(ds=rds[lidx], des=ldes, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[0]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)
    print 'language ' + str(np.mean(lres))

    pwts, _, pres, pceil = bsr.bootstrap_ridge(ds=rds[pidx], des=pdes, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[1]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)

    # pictures within
    print 'pictures: ' + str(np.mean(pres))
    if write:
        map2nifti(thisDS, dataset.vstack([lres, pres])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_corrs.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_wts.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_ceiling.nii.gz'))

    for t in testContrast:
        tstr = '+'.join(t)
        lcorr = lmvpa.testmodel(wts=lwts, des=ldes, ds=rds[lidx], tc=cp.copy(t), use_corr=True)
        pcorr = lmvpa.testmodel(wts=pwts, des=pdes, ds=rds[pidx], tc=cp.copy(t), use_corr=True)
        if write:
            map2nifti(thisDS, dataset.vstack([lcorr, pcorr])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_test_corrs.nii.gz'))

    del lres, pres, lwts, pwts, lceil, pceil
    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    # cwts, cres, cceil = bsr.ridge(rds[pidx], pdes, mu0=mus, cov0=covarmat,
    #                                             part_attr='chunks', mode='test', alphas=alphas[0], single_alpha=True,
    #                                             normalpha=False, corrmin=.2, singcutoff=1e-10, joined=None,
    #                                             use_corr=True)
    cwts, _, cres, cceil = bsr.bootstrap_ridge(ds=crossSet, des=des, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[2]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)
    for t in testContrast:
        tstr = '+'.join(t)
        ccorr = lmvpa.testmodel(wts=cwts, des=des, ds=crossSet, tc=cp.copy(t), use_corr=True)
        if write:
            map2nifti(thisDS, ccorr[0]) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_P2L_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
            map2nifti(thisDS, ccorr[1]) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_L2P_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
    print 'cross: ' + str(np.mean(cres))
    if write:
        map2nifti(thisDS, cres[0]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                     '_P2L_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))
        map2nifti(thisDS, cres[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))

        map2nifti(thisDS, cwts[cwts.chunks==1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_P2L_ridge_alpha_' + str(alphas[2]) + '_wts.nii.gz'))
        map2nifti(thisDS, cwts[cwts.chunks==2]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha' + str(alphas[2]) + '_wts.nii.gz'))

        map2nifti(thisDS, cceil[0]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_P2L_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
        map2nifti(thisDS, cceil[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
    del cres, cwts, cceil
예제 #4
0
def runsub(sub, thisContrast, thisContrastStr, testContrast,
           filterLen, filterOrd, write=False, debug=False,
           alphas=1, roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts)  # adding features

    # we can model out motion and just not use those betas.
    # Ridge
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
                                     design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
                                     regr_attrs=None)
    # 'add_regs': mc_params[sub]

    desX['motion'] = make_dmtx(rds.sa['time_coords'].value, paradigm=None, add_regs=mc_params[sub], drift_model='blank')

    des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)

    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]

    covarmat = None
    mus = None
    lwts, _, lres, lceil = bsr.bootstrap_ridge(ds=rds[lidx], des=ldes, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[0]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)
    print 'language ' + str(np.mean(lres))

    pwts, _, pres, pceil = bsr.bootstrap_ridge(ds=rds[pidx], des=pdes, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[1]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)

    # pictures within
    print 'pictures: ' + str(np.mean(pres))
    if write:
        map2nifti(thisDS, dataset.vstack([lres, pres])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_corrs.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_wts.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_ceiling.nii.gz'))

    for t in testContrast:
        tstr = '+'.join(t)
        lcorr = lmvpa.testmodel(wts=lwts, des=ldes, ds=rds[lidx], tc=cp.copy(t), use_corr=True)
        pcorr = lmvpa.testmodel(wts=pwts, des=pdes, ds=rds[pidx], tc=cp.copy(t), use_corr=True)
        if write:
            map2nifti(thisDS, dataset.vstack([lcorr, pcorr])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_ridge_la_' + str(alphas[0]) + '_pa_' + str(alphas[1]) + '_test_corrs.nii.gz'))

    del lres, pres, lwts, pwts, lceil, pceil
    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    # cwts, cres, cceil = bsr.ridge(rds[pidx], pdes, mu0=mus, cov0=covarmat,
    #                                             part_attr='chunks', mode='test', alphas=alphas[0], single_alpha=True,
    #                                             normalpha=False, corrmin=.2, singcutoff=1e-10, joined=None,
    #                                             use_corr=True)
    cwts, _, cres, cceil = bsr.bootstrap_ridge(ds=crossSet, des=des, chunklen=1, nchunks=1,
                                               cov0=None, mu0=None, part_attr='chunks', mode='test',
                                               alphas=[alphas[2]], single_alpha=True, normalpha=False,
                                               nboots=1, corrmin=.2, singcutoff=1e-10, joined=None,
                                               use_corr=True)
    for t in testContrast:
        tstr = '+'.join(t)
        ccorr = lmvpa.testmodel(wts=cwts, des=des, ds=crossSet, tc=cp.copy(t), use_corr=True)
        if write:
            map2nifti(thisDS, ccorr[0]) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_P2L_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
            map2nifti(thisDS, ccorr[1]) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + tstr +
                                      '_L2P_ridge_alpha_' + str(alphas[2]) + '_test_corr.nii.gz'))
    print 'cross: ' + str(np.mean(cres))
    if write:
        map2nifti(thisDS, cres[0]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                     '_P2L_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))
        map2nifti(thisDS, cres[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha_' + str(alphas[2]) + '_corr.nii.gz'))

        map2nifti(thisDS, cwts[cwts.chunks==1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_P2L_ridge_alpha_' + str(alphas[2]) + '_wts.nii.gz'))
        map2nifti(thisDS, cwts[cwts.chunks==2]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha' + str(alphas[2]) + '_wts.nii.gz'))

        map2nifti(thisDS, cceil[0]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_P2L_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
        map2nifti(thisDS, cceil[1]).to_filename(
            os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                         '_L2P_ridge_alpha_' + str(alphas[2]) + '_ceiling.nii.gz'))
    del cres, cwts, cceil
예제 #5
0
def runsub(sub, thisContrast, filterLen, filterOrd, thisContrastStr, roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub], contrasts) # adding features

    # we can model out motion and just not use those betas.
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    # instead of binarizing each one, make them parametric
    desX, rds = lmvpa.make_designmat(rds, events, time_attr='time_coords', condition_attr=thisContrast,
                                 design_kwargs={'hrf_model': 'canonical', 'drift_model': 'blank'},
                                 regr_attrs=None)
    # want to collapse ap and cr, but have anim separate
    des = lmvpa.make_parammat(desX)

    # set chunklen and nchunks
    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]

    lwts, lres, lceil = bsr.bootstrap_linear(rds[lidx], ldes, part_attr='chunks', mode='test')
    pwts, pres, pceil = bsr.bootstrap_linear(rds[pidx], pdes, part_attr='chunks', mode='test')

    # now I have betas per chunk. could just correlate the betas, or correlate the predictions for corresponding runs
    print 'language ' + str(np.mean(lres))

    # pictures within
    print 'pictures: ' + str(np.mean(pres))
    from mvpa2.base import dataset
    map2nifti(thisDS, dataset.vstack([lres, pres])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_corr.nii.gz'))
    map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_betas.nii.gz'))
    map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_ceiling.nii.gz'))
    del lres, pres, lwts, pwts, lceil, pceil

    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cwts, cres, cceil = bsr.bootstrap_linear(crossSet, des, part_attr='chunks', mode='test')
    print 'cross: ' + str(np.mean(cres))

    map2nifti(thisDS, cres[0]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_univar.nii.gz'))
    map2nifti(thisDS, cres[1]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_univar.nii.gz'))

    map2nifti(thisDS, cwts[0]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_betas.nii.gz'))
    map2nifti(thisDS, cwts[1]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_betas.nii.gz'))

    map2nifti(thisDS, cceil[0]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_P2L_betas.nii.gz'))
    map2nifti(thisDS, cceil[1]).to_filename(
        os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr + '_L2P_betas.nii.gz'))
예제 #6
0
    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])

    #OLS beta extraction
    betas = 'LSA'
    evds = er.fit_event_hrf_model(rds, events, time_attr='time_coords',
                                  condition_attr=('trial_type',  'chunks'),
                                  design_kwargs={'add_regs': mc_params[sub], 'hrf_model': 'canonical'},
                                  return_model=True)

    fds = lmvpa.replacetargets(evds, contrasts, thisContrast)
    fds = fds[fds.targets != '0']
    fds = fds[fds.targets != 'rest']
    rsaresults.append(dsm(fds))

    lidx = fds.chunks < fds.sa['chunks'].unique[len(fds.sa['chunks'].unique)/2]
    pidx = fds.chunks >= fds.sa['chunks'].unique[len(fds.sa['chunks'].unique) / 2]
예제 #7
0
def runsub(sub, thisContrast, r, dstype="raw", roi="grayMatter", filterLen=49, filterOrd=3, write=False):

    if dstype == "raw":
        outdir = "PyMVPA"
        print "working with raw data"
        thisSub = {sub: subList[sub]}
        dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi)
        thisDS = dsdict[sub]
        mc_params = lmvpa.loadmotionparams(paths, thisSub)
        beta_events = lmvpa.loadevents(paths, thisSub)
        # savitsky golay filtering
        sg.sg_filter(thisDS, filterLen, filterOrd)
        # gallant group zscores before regression.

        # zscore w.r.t. rest trials
        # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
        # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
        zscore(thisDS, chunks_attr="chunks")
        print "beta extraction"
        ## BETA EXTRACTION ##
        rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
        evds = er.fit_event_hrf_model(
            rds,
            events,
            time_attr="time_coords",
            condition_attr=("trial_type", "chunks"),
            design_kwargs={"add_regs": mc_params[sub], "hrf_model": "canonical"},
            return_model=True,
        )

        fds = lmvpa.replacetargets(evds, contrasts, thisContrast)
        fds = fds[fds.targets != "0"]
    else:
        outdir = os.path.join("LSS", dstype)
        print "loading betas"
        fds = lmvpa.loadsubbetas(paths, sub, btype=dstype, m=roi)
        fds.sa["targets"] = fds.sa[thisContrast]
        zscore(fds, chunks_attr="chunks")

    fds = lmvpa.sortds(fds)
    print "searchlights"
    ## initialize classifier
    clf = svm.LinearNuSVMC()
    cv = CrossValidation(clf, NFoldPartitioner())
    from mvpa2.measures.searchlight import sphere_searchlight

    cvSL = sphere_searchlight(cv, radius=r)

    # now I have betas per chunk. could just correlate the betas, or correlate the predictions for corresponding runs
    lidx = fds.chunks < fds.sa["chunks"].unique[len(fds.sa["chunks"].unique) / 2]
    pidx = fds.chunks >= fds.sa["chunks"].unique[len(fds.sa["chunks"].unique) / 2]

    lres = sl.run_cv_sl(cvSL, fds[lidx].copy(deep=False))
    pres = sl.run_cv_sl(cvSL, fds[pidx].copy(deep=False))

    if write:
        from mvpa2.base import dataset

        map2nifti(fds, dataset.vstack([lres, pres])).to_filename(
            os.path.join(paths[0], "Maps", outdir, sub + "_" + roi + "_" + thisContrast + "_cvsl.nii.gz")
        )

    del lres, pres, cvSL

    cvSL = sphere_searchlight(cv, radius=r)
    crossSet = fds.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cres = sl.run_cv_sl(cvSL, crossSet.copy(deep=False))
    if write:
        map2nifti(fds, cres[0]).to_filename(
            os.path.join(paths[0], "Maps", outdir, sub + "_" + roi + "_" + (thisContrast) + "_P2L.nii.gz")
        )
        map2nifti(fds, cres[1]).to_filename(
            os.path.join(paths[0], "Maps", outdir, sub + "_" + roi + "_" + (thisContrast) + "_L2P.nii.gz")
        )
예제 #8
0
def runsub(sub,
           thisContrast,
           filterLen,
           filterOrd,
           thisContrastStr,
           roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub],
                                     contrasts)  # adding features

    # we can model out motion and just not use those betas.
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    # instead of binarizing each one, make them parametric
    desX, rds = lmvpa.make_designmat(rds,
                                     events,
                                     time_attr='time_coords',
                                     condition_attr=thisContrast,
                                     design_kwargs={
                                         'hrf_model': 'canonical',
                                         'drift_model': 'blank'
                                     },
                                     regr_attrs=None)
    # want to collapse ap and cr, but have anim separate
    des = lmvpa.make_parammat(desX)

    # set chunklen and nchunks
    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(
        thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(
        thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]

    lwts, lres, lceil = bsr.bootstrap_linear(rds[lidx],
                                             ldes,
                                             part_attr='chunks',
                                             mode='test')
    pwts, pres, pceil = bsr.bootstrap_linear(rds[pidx],
                                             pdes,
                                             part_attr='chunks',
                                             mode='test')

    # now I have betas per chunk. could just correlate the betas, or correlate the predictions for corresponding runs
    print 'language ' + str(np.mean(lres))

    # pictures within
    print 'pictures: ' + str(np.mean(pres))
    from mvpa2.base import dataset
    map2nifti(thisDS, dataset.vstack([lres, pres])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_corr.nii.gz'))
    map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_betas.nii.gz'))
    map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
        .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                  '_univar_ceiling.nii.gz'))
    del lres, pres, lwts, pwts, lceil, pceil

    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cwts, cres, cceil = bsr.bootstrap_linear(crossSet,
                                             des,
                                             part_attr='chunks',
                                             mode='test')
    print 'cross: ' + str(np.mean(cres))

    map2nifti(thisDS, cres[0]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_P2L_univar.nii.gz'))
    map2nifti(thisDS, cres[1]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_L2P_univar.nii.gz'))

    map2nifti(thisDS, cwts[0]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_P2L_betas.nii.gz'))
    map2nifti(thisDS, cwts[1]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_L2P_betas.nii.gz'))

    map2nifti(thisDS, cceil[0]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_P2L_betas.nii.gz'))
    map2nifti(thisDS, cceil[1]).to_filename(
        os.path.join(
            paths[0], 'Maps', 'Encoding',
            sub + '_' + roi + '_' + thisContrastStr + '_L2P_betas.nii.gz'))
예제 #9
0
    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])

    #OLS beta extraction
    betas = 'LSA'
    evds = er.fit_event_hrf_model(rds,
                                  events,
                                  time_attr='time_coords',
                                  condition_attr=('trial_type', 'chunks'),
                                  design_kwargs={
                                      'add_regs': mc_params[sub],
                                      'hrf_model': 'canonical'
                                  },
                                  return_model=True)

    fds = lmvpa.replacetargets(evds, contrasts, thisContrast)
    fds = fds[fds.targets != '0']
예제 #10
0
def runsub(sub,
           thisContrast,
           thisContrastStr,
           filterLen,
           filterOrd,
           paramEst,
           chunklen,
           alphas=np.logspace(0, 3, 20),
           debug=False,
           write=False,
           roi='grayMatter'):
    thisSub = {sub: subList[sub]}
    mc_params = lmvpa.loadmotionparams(paths, thisSub)
    beta_events = lmvpa.loadevents(paths, thisSub)
    dsdict = lmvpa.loadsubdata(paths, thisSub, m=roi, c='trial_type')
    thisDS = dsdict[sub]

    # savitsky golay filtering
    sg.sg_filter(thisDS, filterLen, filterOrd)
    # gallant group zscores before regression.

    # zscore w.r.t. rest trials
    # zscore(thisDS, param_est=('targets', ['rest']), chunks_attr='chunks')
    # zscore entire set. if done chunk-wise, there is no double-dipping (since we leave a chunk out at a time).
    zscore(thisDS, chunks_attr='chunks')

    # kay method: leave out a model run, use it to fit an HRF for each voxel
    # huth method: essentially use FIR
    # mumford method: deconvolution with canonical HRF

    # refit events and regress...
    # get timing data from timing files
    # rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub])
    rds, events = lmvpa.amendtimings(thisDS.copy(), beta_events[sub],
                                     contrasts)  # adding features

    # we can model out motion and just not use those betas.
    # Ridge
    if isinstance(thisContrast, basestring):
        thisContrast = [thisContrast]
    # instead of binarizing each one, make them parametric
    desX, rds = lmvpa.make_designmat(rds,
                                     events,
                                     time_attr='time_coords',
                                     condition_attr=thisContrast,
                                     design_kwargs={
                                         'hrf_model': 'canonical',
                                         'drift_model': 'blank'
                                     },
                                     regr_attrs=None)
    # want to collapse ap and cr, but have anim separate
    desX['motion'] = make_dmtx(rds.sa['time_coords'].value,
                               paradigm=None,
                               add_regs=mc_params[sub],
                               drift_model='blank')

    des = lmvpa.make_parammat(desX, hrf='canonical', zscore=True)

    # set chunklen and nchunks
    # split by language and pictures
    lidx = thisDS.chunks < thisDS.sa['chunks'].unique[len(
        thisDS.sa['chunks'].unique) / 2]
    pidx = thisDS.chunks >= thisDS.sa['chunks'].unique[len(
        thisDS.sa['chunks'].unique) / 2]
    ldes = cp.copy(des)
    pdes = cp.copy(des)

    ldes.matrix = ldes.matrix[lidx]
    pdes.matrix = pdes.matrix[pidx]
    nchunks = int(len(thisDS) * paramEst / chunklen)
    nboots = 50
    covarmat = None
    mus = None
    lwts, lalphas, lres, lceil = bsr.bootstrap_ridge(rds[lidx],
                                                     ldes,
                                                     chunklen=chunklen,
                                                     nchunks=nchunks,
                                                     cov0=covarmat,
                                                     mu0=mus,
                                                     part_attr='chunks',
                                                     mode='test',
                                                     alphas=alphas,
                                                     single_alpha=True,
                                                     normalpha=False,
                                                     nboots=nboots,
                                                     corrmin=.2,
                                                     singcutoff=1e-10,
                                                     joined=None,
                                                     plot=debug,
                                                     use_corr=True)

    pwts, palphas, pres, pceil = bsr.bootstrap_ridge(rds[pidx],
                                                     pdes,
                                                     chunklen=chunklen,
                                                     nchunks=nchunks,
                                                     part_attr='chunks',
                                                     mode='test',
                                                     alphas=alphas,
                                                     single_alpha=True,
                                                     normalpha=False,
                                                     nboots=nboots,
                                                     corrmin=.2,
                                                     singcutoff=1e-10,
                                                     joined=None,
                                                     plot=debug,
                                                     use_corr=True)
    print 'language ' + str(np.mean(lres))

    # pictures within
    print 'pictures: ' + str(np.mean(pres))

    # need to change outstring
    if write:
        from mvpa2.base import dataset
        map2nifti(thisDS, dataset.vstack([lres, pres])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_corrs.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lwts, pwts])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_weights.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lalphas, palphas])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_alphas.nii.gz'))
        map2nifti(thisDS, dataset.vstack([lceil, pceil])) \
            .to_filename(os.path.join(paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' + thisContrastStr +
                                      '_ridge_ceiling.nii.gz'))

    del lres, pres, lwts, pwts, lalphas, palphas, lceil, pceil
    crossSet = thisDS.copy()
    crossSet.chunks[lidx] = 1
    crossSet.chunks[pidx] = 2
    cwts, calphas, cres, cceil = bsr.bootstrap_ridge(crossSet,
                                                     des,
                                                     chunklen=chunklen,
                                                     nchunks=nchunks,
                                                     part_attr='chunks',
                                                     mode='test',
                                                     alphas=alphas,
                                                     single_alpha=True,
                                                     normalpha=False,
                                                     nboots=nboots,
                                                     corrmin=.2,
                                                     singcutoff=1e-10,
                                                     joined=None,
                                                     use_corr=True)
    print 'cross: ' + str(np.mean(cres))
    if write:
        map2nifti(thisDS, cres[0]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_P2L_ridge_corr.nii.gz'))
        map2nifti(thisDS, cres[1]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_L2P_ridge_corr.nii.gz'))

        map2nifti(thisDS, cwts[0]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_P2L_ridge_weights.nii.gz'))
        map2nifti(thisDS, cwts[1]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_L2P_ridge_weights.nii.gz'))

        map2nifti(thisDS, calphas[calphas.chunks == 1]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_P2L_ridge_alphas.nii.gz'))
        map2nifti(thisDS, calphas[calphas.chunks == 2]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_L2P_ridge_alphas.nii.gz'))

        map2nifti(thisDS, cceil[0]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_P2L_ridge_ceiling.nii.gz'))
        map2nifti(thisDS, cceil[1]).to_filename(
            os.path.join(
                paths[0], 'Maps', 'Encoding', sub + '_' + roi + '_' +
                thisContrastStr + '_L2P_ridge_ceiling.nii.gz'))
    del cres, cwts, calphas, cceil