Beispiel #1
0
def parse_spm5_preproc(work_dir, step):
    doc = {}
    if hasattr(step, 'spatial') and hasattr(step.spatial, 'realign'):
        realign = step.spatial.realign.estwrite
        motion = []
        if len(realign.data[0].shape) == 0:
            realign = [realign]
        else:
            realign = realign.data
            for session in realign:
                data_dir = find_data_dir(work_dir, check_path(session[0]))
                motion.append(glob.glob(os.path.join(data_dir, 'rp_*.txt'))[0])
            doc['motion'] = motion
    if hasattr(step, 'spatial') and isinstance(step.spatial, np.ndarray):
        doc['anatomy'] = makeup_path(work_dir,
                                     check_path(step.spatial[0].preproc.data))
        doc['wmanatomy'] = prefix_filename(
            makeup_path(
                work_dir,
                check_path(step.spatial[1].normalise.write.subj.resample)),
            'w')
    if hasattr(step, 'temporal'):
        doc['n_slices'] = int(step.temporal.st.nslices)
        doc['ref_slice'] = int(step.temporal.st.refslice)
        doc['slice_order'] = step.temporal.st.so.tolist()
        doc['ta'] = float(step.temporal.st.ta)
        doc['tr'] = float(step.temporal.st.tr)
        doc['bold'] = []
        doc['swabold'] = []
        if len(step.temporal.st.scans[0].shape) == 0:
            bold = [step.temporal.st.scans]
        else:
            bold = step.temporal.st.scans
        for session in bold:
            data_dir = find_data_dir(work_dir, str(session[0]))
            doc['bold'].append(
                check_paths([
                    os.path.join(data_dir,
                                 os.path.split(str(x))[1]) for x in session
                ]))
            doc['swabold'].append(
                check_paths([
                    prefix_filename(
                        os.path.join(data_dir,
                                     os.path.split(str(x))[1]), 'swa')
                    for x in session
                ]))
        doc['n_scans'] = [len(s) for s in doc['bold']]
    return doc
Beispiel #2
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def parse_spm8_preproc(work_dir, step):
    doc = {}

    if hasattr(step, 'spatial') and hasattr(step.spatial, 'preproc'):
        doc['anatomy'] = makeup_path(
            work_dir, check_path(step.spatial.preproc.data))
        doc['wmanatomy'] = prefix_filename(doc['anatomy'], 'wm')

    if hasattr(step, 'temporal'):
        doc['n_slices'] = int(step.temporal.st.nslices)
        doc['ref_slice'] = int(step.temporal.st.refslice)
        doc['slice_order'] = step.temporal.st.so.tolist()
        doc['ta'] = float(step.temporal.st.ta)
        doc['tr'] = float(step.temporal.st.tr)
        doc['bold'] = []
        doc['swabold'] = []
        if len(step.temporal.st.scans[0].shape) == 0:
            bold = [step.temporal.st.scans]
        else:
            bold = step.temporal.st.scans
        for session in bold:
            data_dir = find_data_dir(work_dir, str(session[0]))
            doc['bold'].append(check_paths(
                [os.path.join(data_dir, os.path.split(str(x))[1])
                 for x in session]))
            doc['swabold'].append(check_paths(
                [prefix_filename(os.path.join(
                    data_dir, os.path.split(str(x))[1]), 'swa')
                for x in session]))
        doc['n_scans'] = [len(s) for s in doc['bold']]
    return doc
Beispiel #3
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def parse_spm5_preproc(work_dir, step):
    doc = {}
    if hasattr(step, 'spatial') and hasattr(step.spatial, 'realign'):
        realign = step.spatial.realign.estwrite
        motion = []
        if len(realign.data[0].shape) == 0:
            realign = [realign]
        else:
            realign = realign.data
            for session in realign:
                data_dir = find_data_dir(work_dir, check_path(session[0]))
                motion.append(glob.glob(os.path.join(data_dir, 'rp_*.txt'))[0])
            doc['motion'] = motion
    if hasattr(step, 'spatial') and isinstance(step.spatial, np.ndarray):
        doc['anatomy'] = makeup_path(
            work_dir, check_path(step.spatial[0].preproc.data))
        doc['wmanatomy'] = prefix_filename(makeup_path(
            work_dir,
            check_path(step.spatial[1].normalise.write.subj.resample)),
            'w')
    if hasattr(step, 'temporal'):
        doc['n_slices'] = int(step.temporal.st.nslices)
        doc['ref_slice'] = int(step.temporal.st.refslice)
        doc['slice_order'] = step.temporal.st.so.tolist()
        doc['ta'] = float(step.temporal.st.ta)
        doc['tr'] = float(step.temporal.st.tr)
        doc['bold'] = []
        doc['swabold'] = []
        if len(step.temporal.st.scans[0].shape) == 0:
            bold = [step.temporal.st.scans]
        else:
            bold = step.temporal.st.scans
        for session in bold:
            data_dir = find_data_dir(work_dir, str(session[0]))
            doc['bold'].append(check_paths(
                [os.path.join(data_dir, os.path.split(str(x))[1])
                 for x in session]))
            doc['swabold'].append(check_paths(
                [prefix_filename(os.path.join(
                    data_dir, os.path.split(str(x))[1]), 'swa')
                for x in session]))
        doc['n_scans'] = [len(s) for s in doc['bold']]
    return doc
Beispiel #4
0
def get_intra_preproc(mat_file, work_dir, n_scans, memory=Memory(None)):
    mat = memory.cache(load_matfile)(mat_file)['SPM']
    preproc = {}

    get_motion_file = False
    if len(n_scans) > 1:
        preproc['motion'] = []
        for session in mat.Sess:
            preproc['motion'].append(session.C.C.tolist())
            if session.C.C.size == 0:
                get_motion_file = True
    else:
        preproc['motion'] = [mat.Sess.C.C.tolist()]
        if mat.Sess.C.C.size == 0:
            get_motion_file = True

    swabold = check_paths(mat.xY.P)
    if len(nb.load(makeup_path(work_dir, swabold[0])).shape) == 4:
        swabold = np.unique(swabold)
    else:
        swabold = np.split(swabold, np.cumsum(n_scans)[:-1])

    if get_motion_file:
        preproc['motion'] = []

    for session in swabold:
        session_dir = find_data_dir(work_dir, check_path(session[0]))
        if get_motion_file:
            motion_file = glob.glob(os.path.join(session_dir, 'rp_*.txt'))[0]
            motion = np.fromfile(motion_file, sep=' ')
            motion = motion.reshape(motion.shape[0] / 6, 6)
            preproc['motion'].append(motion)

        if isinstance(session, (list, np.ndarray)):
            scans = [
                os.path.join(session_dir,
                             os.path.split(scan)[1].strip())
                for scan in session
            ]
            preproc.setdefault('swabold', []).append(scans)
            preproc.setdefault('abold', []).append(
                [strip_prefix_filename(scan, 2) for scan in scans])
            preproc.setdefault('bold', []).append(
                [strip_prefix_filename(scan, 3) for scan in scans])
        else:
            preproc.setdefault('swabold', []).append(session)
            preproc.setdefault('abold',
                               []).append(strip_prefix_filename(session, 2))
            preproc.setdefault('bold',
                               []).append(strip_prefix_filename(session, 3))

    return preproc
Beispiel #5
0
def get_intra_preproc(mat_file, work_dir, n_scans, memory=Memory(None)):
    mat = memory.cache(load_matfile)(mat_file)['SPM']
    preproc = {}

    get_motion_file = False
    if len(n_scans) > 1:
        preproc['motion'] = []
        for session in mat.Sess:
            preproc['motion'].append(session.C.C.tolist())
            if session.C.C.size == 0:
                get_motion_file = True
    else:
        preproc['motion'] = [mat.Sess.C.C.tolist()]
        if mat.Sess.C.C.size == 0:
            get_motion_file = True

    swabold = check_paths(mat.xY.P)
    if len(nb.load(makeup_path(work_dir, swabold[0])).shape) == 4:
        swabold = np.unique(swabold)
    else:
        swabold = np.split(swabold, np.cumsum(n_scans)[:-1])

    if get_motion_file:
        preproc['motion'] = []

    for session in swabold:
        session_dir = find_data_dir(work_dir, check_path(session[0]))
        if get_motion_file:
            motion_file = glob.glob(os.path.join(session_dir, 'rp_*.txt'))[0]
            motion = np.fromfile(motion_file, sep=' ')
            motion = motion.reshape(motion.shape[0] / 6, 6)
            preproc['motion'].append(motion)

        if isinstance(session, (list, np.ndarray)):
            scans = [os.path.join(session_dir, os.path.split(scan)[1].strip())
                     for scan in session]
            preproc.setdefault('swabold', []).append(scans)
            preproc.setdefault('abold', []).append(
                [strip_prefix_filename(scan, 2) for scan in scans])
            preproc.setdefault('bold', []).append(
                [strip_prefix_filename(scan, 3) for scan in scans])
        else:
            preproc.setdefault('swabold', []).append(session)
            preproc.setdefault('abold', []).append(
                strip_prefix_filename(session, 2))
            preproc.setdefault('bold', []).append(
                strip_prefix_filename(session, 3))

    return preproc
Beispiel #6
0
def parse_spm8_preproc(work_dir, step):
    doc = {}

    if hasattr(step, 'spatial') and hasattr(step.spatial, 'preproc'):
        doc['anatomy'] = makeup_path(work_dir,
                                     check_path(step.spatial.preproc.data))
        doc['wmanatomy'] = prefix_filename(doc['anatomy'], 'wm')

    if hasattr(step, 'temporal'):
        doc['n_slices'] = int(step.temporal.st.nslices)
        doc['ref_slice'] = int(step.temporal.st.refslice)
        doc['slice_order'] = step.temporal.st.so.tolist()
        doc['ta'] = float(step.temporal.st.ta)
        doc['tr'] = float(step.temporal.st.tr)
        doc['bold'] = []
        doc['swabold'] = []
        if len(step.temporal.st.scans[0].shape) == 0:
            bold = [step.temporal.st.scans]
        else:
            bold = step.temporal.st.scans
        for session in bold:
            data_dir = find_data_dir(work_dir, str(session[0]))
            doc['bold'].append(
                check_paths([
                    os.path.join(data_dir,
                                 os.path.split(str(x))[1]) for x in session
                ]))
            doc['swabold'].append(
                check_paths([
                    prefix_filename(
                        os.path.join(data_dir,
                                     os.path.split(str(x))[1]), 'swa')
                    for x in session
                ]))
        doc['n_scans'] = [len(s) for s in doc['bold']]
    return doc