def test_Binarize_outputs():
    output_map = dict(binary_file=dict(),
    count_file=dict(),
    )
    outputs = Binarize.output_spec()

    for key, metadata in output_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(outputs.traits()[key], metakey), value
示例#2
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def test_Binarize_outputs():
    output_map = dict(
        binary_file=dict(),
        count_file=dict(),
    )
    outputs = Binarize.output_spec()

    for key, metadata in output_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_Binarize_inputs():
    input_map = dict(abs=dict(argstr='--abs',
    ),
    args=dict(argstr='%s',
    ),
    bin_col_num=dict(argstr='--bincol',
    ),
    bin_val=dict(argstr='--binval %d',
    ),
    bin_val_not=dict(argstr='--binvalnot %d',
    ),
    binary_file=dict(argstr='--o %s',
    genfile=True,
    ),
    count_file=dict(argstr='--count %s',
    ),
    dilate=dict(argstr='--dilate %d',
    ),
    environ=dict(nohash=True,
    usedefault=True,
    ),
    erode=dict(argstr='--erode  %d',
    ),
    erode2d=dict(argstr='--erode2d %d',
    ),
    frame_no=dict(argstr='--frame %s',
    ),
    ignore_exception=dict(nohash=True,
    usedefault=True,
    ),
    in_file=dict(argstr='--i %s',
    copyfile=False,
    mandatory=True,
    ),
    invert=dict(argstr='--inv',
    ),
    mask_file=dict(argstr='--mask maskvol',
    ),
    mask_thresh=dict(argstr='--mask-thresh %f',
    ),
    match=dict(argstr='--match %d...',
    ),
    max=dict(argstr='--max %f',
    xor=['wm_ven_csf'],
    ),
    merge_file=dict(argstr='--merge %s',
    ),
    min=dict(argstr='--min %f',
    xor=['wm_ven_csf'],
    ),
    out_type=dict(argstr='',
    ),
    rmax=dict(argstr='--rmax %f',
    ),
    rmin=dict(argstr='--rmin %f',
    ),
    subjects_dir=dict(),
    terminal_output=dict(nohash=True,
    ),
    ventricles=dict(argstr='--ventricles',
    ),
    wm=dict(argstr='--wm',
    ),
    wm_ven_csf=dict(argstr='--wm+vcsf',
    xor=['min', 'max'],
    ),
    zero_edges=dict(argstr='--zero-edges',
    ),
    zero_slice_edge=dict(argstr='--zero-slice-edges',
    ),
    )
    inputs = Binarize.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value
示例#4
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## Level 2

# merge param estimates across all subjects per seed
merge = Node(Merge(dimension='t'), name='merge')

# FSL randomise for higher level analysis
highermodel = Node(Randomise(tfce=True,
                             raw_stats_imgs=True,
                             design_mat=group_mat,
                             tcon=group_con),
                   name='highermodel')

## Cluster results

# make binary masks of sig clusters
binarize = Node(Binarize(min=0.95, max=1.0),
                name='binarize',
                iterfield='in_file')

# mask T-map before clustering
mask_tmaps = Node(ApplyMask(), name='mask_tmaps')

# clusterize and extract cluster stats/peaks
clusterize = Node(Cluster(threshold=2.3,
                          out_index_file='outindex.nii',
                          out_localmax_txt_file='localmax.txt'),
                  name='clusterize')

# make pictures if time

# In[ ]:
示例#5
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def test_Binarize_inputs():
    input_map = dict(
        abs=dict(argstr='--abs', ),
        args=dict(argstr='%s', ),
        bin_col_num=dict(argstr='--bincol', ),
        bin_val=dict(argstr='--binval %d', ),
        bin_val_not=dict(argstr='--binvalnot %d', ),
        binary_file=dict(
            argstr='--o %s',
            genfile=True,
        ),
        count_file=dict(argstr='--count %s', ),
        dilate=dict(argstr='--dilate %d', ),
        environ=dict(
            nohash=True,
            usedefault=True,
        ),
        erode=dict(argstr='--erode  %d', ),
        erode2d=dict(argstr='--erode2d %d', ),
        frame_no=dict(argstr='--frame %s', ),
        ignore_exception=dict(
            nohash=True,
            usedefault=True,
        ),
        in_file=dict(
            argstr='--i %s',
            copyfile=False,
            mandatory=True,
        ),
        invert=dict(argstr='--inv', ),
        mask_file=dict(argstr='--mask maskvol', ),
        mask_thresh=dict(argstr='--mask-thresh %f', ),
        match=dict(argstr='--match %d...', ),
        max=dict(
            argstr='--max %f',
            xor=['wm_ven_csf'],
        ),
        merge_file=dict(argstr='--merge %s', ),
        min=dict(
            argstr='--min %f',
            xor=['wm_ven_csf'],
        ),
        out_type=dict(argstr='', ),
        rmax=dict(argstr='--rmax %f', ),
        rmin=dict(argstr='--rmin %f', ),
        subjects_dir=dict(),
        terminal_output=dict(
            mandatory=True,
            nohash=True,
        ),
        ventricles=dict(argstr='--ventricles', ),
        wm=dict(argstr='--wm', ),
        wm_ven_csf=dict(
            argstr='--wm+vcsf',
            xor=['min', 'max'],
        ),
        zero_edges=dict(argstr='--zero-edges', ),
        zero_slice_edge=dict(argstr='--zero-slice-edges', ),
    )
    inputs = Binarize.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value