def test_JistBrainMp2rageSkullStripping_outputs():
output_map = dict(outBrain=dict(),
outMasked=dict(),
outMasked2=dict(),
outMasked3=dict(),
)
outputs = JistBrainMp2rageSkullStripping.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_JistBrainMp2rageSkullStripping_inputs():
input_map = dict(
args=dict(argstr='%s', ),
environ=dict(
nohash=True,
usedefault=True,
),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
inFilter=dict(argstr='--inFilter %s', ),
inSecond=dict(argstr='--inSecond %s', ),
inSkip=dict(argstr='--inSkip %s', ),
inT1=dict(argstr='--inT1 %s', ),
inT1weighted=dict(argstr='--inT1weighted %s', ),
null=dict(argstr='--null %s', ),
outBrain=dict(
argstr='--outBrain %s',
hash_files=False,
),
outMasked=dict(
argstr='--outMasked %s',
hash_files=False,
),
outMasked2=dict(
argstr='--outMasked2 %s',
hash_files=False,
),
outMasked3=dict(
argstr='--outMasked3 %s',
hash_files=False,
),
terminal_output=dict(
mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d', ),
xMaxProcess=dict(
argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s', ),
)
inputs = JistBrainMp2rageSkullStripping.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_JistBrainMp2rageSkullStripping_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inFilter=dict(argstr='--inFilter %s',
),
inSecond=dict(argstr='--inSecond %s',
),
inSkip=dict(argstr='--inSkip %s',
),
inT1=dict(argstr='--inT1 %s',
),
inT1weighted=dict(argstr='--inT1weighted %s',
),
null=dict(argstr='--null %s',
),
outBrain=dict(argstr='--outBrain %s',
hash_files=False,
),
outMasked=dict(argstr='--outMasked %s',
hash_files=False,
),
outMasked2=dict(argstr='--outMasked2 %s',
hash_files=False,
),
outMasked3=dict(argstr='--outMasked3 %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistBrainMp2rageSkullStripping.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 create_mp2rage_pipeline(name='mp2rage'):
# workflow
mp2rage = Workflow('mp2rage')
# inputnode
inputnode=Node(util.IdentityInterface(fields=['inv2',
'uni',
't1map']),
name='inputnode')
# outputnode
outputnode=Node(util.IdentityInterface(fields=['uni_masked',
'background_mask',
'uni_stripped',
'skullstrip_mask',
]),
name='outputnode')
#get filenames from list
def return_list_element(x):
x_file=x[0]
return x_file
get_uni= Node(util.Function(input_names=["x"],
output_names=["x_file"],
function = return_list_element), name="get_uni")
get_t1= Node(util.Function(input_names=["x"],
output_names=["x_file"],
function = return_list_element), name="get_t1")
get_inv2= Node(util.Function(input_names=["x"],
output_names=["x_file"],
function = return_list_element), name="get_inv2")
# remove background noise
background = Node(JistIntensityMp2rageMasking(outMasked=True,
outMasked2=True,
outSignal2=True),
name='background')
# skullstrip
# strip = Node(MedicAlgorithmSPECTRE2010(outStripped=True,
# outMask=True,
# outOriginal=True,
# inOutput='true',
# inFind='true',
# inMMC=4
# ),
# name='strip')
strip = Node(JistBrainMp2rageSkullStripping(outBrain=True, outMasked2=True),name='strip')
# connections
mp2rage.connect([(inputnode, get_uni, [('uni','x')]),
(inputnode, get_t1, [('t1map','x')]),
(inputnode, get_inv2, [('inv2','x')]),
(get_inv2, background, [('x_file', 'inSecond')]),
(get_t1, background, [('x_file', 'inQuantitative')]),
(get_uni, background, [('x_file','inT1weighted')]),
(background, strip, [('outMasked2','inT1weighted')]),
(get_inv2, strip, [('x_file', 'inSecond')]),
(background, outputnode, [('outMasked2','uni_masked'),
('outSignal2','background_mask')]),
(strip, outputnode, [('outMasked2','uni_stripped'),
('outBrain', 'skullstrip_mask')
])
])
return mp2rage