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_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
## 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[ ]:
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