def test_SliceTimer_outputs():
output_map = dict(slice_time_corrected_file=dict(), )
outputs = SliceTimer.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_SliceTimer_outputs():
output_map = dict(slice_time_corrected_file=dict(),
)
outputs = SliceTimer.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_SliceTimer_inputs():
input_map = dict(ignore_exception=dict(nohash=True,
usedefault=True,
),
index_dir=dict(argstr='--down',
),
args=dict(argstr='%s',
),
out_file=dict(argstr='--out=%s',
hash_files=False,
genfile=True,
),
custom_timings=dict(argstr='--tcustom=%s',
),
time_repetition=dict(argstr='--repeat=%f',
),
slice_direction=dict(argstr='--direction=%d',
),
custom_order=dict(argstr='--ocustom=%s',
),
terminal_output=dict(mandatory=True,
nohash=True,
),
environ=dict(nohash=True,
usedefault=True,
),
in_file=dict(position=0,
mandatory=True,
argstr='--in=%s',
),
global_shift=dict(argstr='--tglobal',
),
output_type=dict(),
interleaved=dict(argstr='--odd',
),
)
inputs = SliceTimer.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
def test_SliceTimer_inputs():
input_map = dict(
args=dict(argstr='%s', ),
custom_order=dict(argstr='--ocustom=%s', ),
custom_timings=dict(argstr='--tcustom=%s', ),
environ=dict(
nohash=True,
usedefault=True,
),
global_shift=dict(argstr='--tglobal', ),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
in_file=dict(
argstr='--in=%s',
mandatory=True,
position=0,
),
index_dir=dict(argstr='--down', ),
interleaved=dict(argstr='--odd', ),
out_file=dict(
argstr='--out=%s',
genfile=True,
hash_files=False,
),
output_type=dict(),
slice_direction=dict(argstr='--direction=%d', ),
terminal_output=dict(
mandatory=True,
nohash=True,
),
time_repetition=dict(argstr='--repeat=%f', ),
)
inputs = SliceTimer.input_spec()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value
# Reorient to standard space using FSL
reorientfunc = Node(Reorient2Std(), name='reorientfunc')
reorientstruct = Node(Reorient2Std(), name='reorientstruct')
# Reslice- using MRI_convert
reslice = Node(MRIConvert(vox_size=resampled_voxel_size, out_type='nii'),
name='reslice')
# Segment structural scan
#segment = Node(Segment(affine_regularization='none'), name='segment')
segment = Node(FAST(no_bias=True, segments=True, number_classes=3),
name='segment')
#Slice timing correction based on interleaved acquisition using FSL
slicetime_correct = Node(SliceTimer(interleaved=interleave,
slice_direction=slice_dir,
time_repetition=TR),
name='slicetime_correct')
# Motion correction
motion_correct = Node(MCFLIRT(save_plots=True, mean_vol=True),
name='motion_correct')
# Registration- using FLIRT
# The BOLD image is 'in_file', the anat is 'reference', the output is 'out_file'
coreg1 = Node(FLIRT(), name='coreg1')
coreg2 = Node(FLIRT(apply_xfm=True), name='coreg2')
# make binary mask
# structural is the 'in_file', output is 'binary_file'
binarize_struct = Node(Binarize(dilate=mask_dilation,