def test_JSONFileGrabber_outputs():
output_map = dict()
outputs = JSONFileGrabber.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_JSONFileGrabber_outputs():
output_map = dict()
outputs = JSONFileGrabber.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_JSONFileGrabber_inputs():
input_map = dict(defaults=dict(),
ignore_exception=dict(nohash=True,
usedefault=True,
),
in_file=dict(),
)
inputs = JSONFileGrabber.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_JSONFileGrabber_inputs():
input_map = dict(
defaults=dict(),
ignore_exception=dict(
nohash=True,
usedefault=True,
),
in_file=dict(),
)
inputs = JSONFileGrabber.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 sdc_fmb(name='fmb_correction',
interp='Linear',
fugue_params=dict(smooth3d=2.0)):
"""
SDC stands for susceptibility distortion correction. FMB stands for
fieldmap-based.
The fieldmap based (FMB) method implements SDC by using a mapping of the
B0 field as proposed by [Jezzard95]_. This workflow uses the implementation
of FSL (`FUGUE <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE>`_). Phase
unwrapping is performed using `PRELUDE
<http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fugue/prelude.html>`_
[Jenkinson03]_. Preparation of the fieldmap is performed reproducing the
script in FSL `fsl_prepare_fieldmap
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide#SIEMENS_data>`_.
Example
-------
>>> from nipype.workflows.dmri.fsl.artifacts import sdc_fmb
>>> fmb = sdc_fmb()
>>> fmb.inputs.inputnode.in_file = 'diffusion.nii'
>>> fmb.inputs.inputnode.in_ref = list(range(0, 30, 6))
>>> fmb.inputs.inputnode.in_mask = 'mask.nii'
>>> fmb.inputs.inputnode.bmap_mag = 'magnitude.nii'
>>> fmb.inputs.inputnode.bmap_pha = 'phase.nii'
>>> fmb.inputs.inputnode.settings = 'epi_param.txt'
>>> fmb.run() # doctest: +SKIP
.. warning:: Only SIEMENS format fieldmaps are supported.
.. admonition:: References
.. [Jezzard95] Jezzard P, and Balaban RS, `Correction for geometric
distortion in echo planar images from B0 field variations
<https://doi.org/10.1002/mrm.1910340111>`_,
MRM 34(1):65-73. (1995). doi: 10.1002/mrm.1910340111.
.. [Jenkinson03] Jenkinson M., `Fast, automated, N-dimensional
phase-unwrapping algorithm <https://doi.org/10.1002/mrm.10354>`_,
MRM 49(1):193-197, 2003, doi: 10.1002/mrm.10354.
"""
epi_defaults = {
'delta_te': 2.46e-3,
'echospacing': 0.77e-3,
'acc_factor': 2,
'enc_dir': u'AP'
}
inputnode = pe.Node(niu.IdentityInterface(fields=[
'in_file', 'in_ref', 'in_mask', 'bmap_pha', 'bmap_mag', 'settings'
]),
name='inputnode')
outputnode = pe.Node(
niu.IdentityInterface(fields=['out_file', 'out_vsm', 'out_warp']),
name='outputnode')
r_params = pe.Node(JSONFileGrabber(defaults=epi_defaults),
name='SettingsGrabber')
eff_echo = pe.Node(niu.Function(function=_eff_t_echo,
input_names=['echospacing', 'acc_factor'],
output_names=['eff_echo']),
name='EffEcho')
firstmag = pe.Node(fsl.ExtractROI(t_min=0, t_size=1), name='GetFirst')
n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='Bias')
bet = pe.Node(fsl.BET(frac=0.4, mask=True), name='BrainExtraction')
dilate = pe.Node(fsl.maths.MathsCommand(nan2zeros=True,
args='-kernel sphere 5 -dilM'),
name='MskDilate')
pha2rads = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_file'],
function=siemens2rads),
name='PreparePhase')
prelude = pe.Node(fsl.PRELUDE(process3d=True), name='PhaseUnwrap')
rad2rsec = pe.Node(niu.Function(input_names=['in_file', 'delta_te'],
output_names=['out_file'],
function=rads2radsec),
name='ToRadSec')
baseline = pe.Node(niu.Function(input_names=['in_file', 'index'],
output_names=['out_file'],
function=time_avg),
name='Baseline')
fmm2b0 = pe.Node(ants.Registration(output_warped_image=True),
name="FMm_to_B0")
fmm2b0.inputs.transforms = ['Rigid'] * 2
fmm2b0.inputs.transform_parameters = [(1.0, )] * 2
fmm2b0.inputs.number_of_iterations = [[50], [20]]
fmm2b0.inputs.dimension = 3
fmm2b0.inputs.metric = ['Mattes', 'Mattes']
fmm2b0.inputs.metric_weight = [1.0] * 2
fmm2b0.inputs.radius_or_number_of_bins = [64, 64]
fmm2b0.inputs.sampling_strategy = ['Regular', 'Random']
fmm2b0.inputs.sampling_percentage = [None, 0.2]
fmm2b0.inputs.convergence_threshold = [1.e-5, 1.e-8]
fmm2b0.inputs.convergence_window_size = [20, 10]
fmm2b0.inputs.smoothing_sigmas = [[6.0], [2.0]]
fmm2b0.inputs.sigma_units = ['vox'] * 2
fmm2b0.inputs.shrink_factors = [[6], [1]] # ,[1] ]
fmm2b0.inputs.use_estimate_learning_rate_once = [True] * 2
fmm2b0.inputs.use_histogram_matching = [True] * 2
fmm2b0.inputs.initial_moving_transform_com = 0
fmm2b0.inputs.collapse_output_transforms = True
fmm2b0.inputs.winsorize_upper_quantile = 0.995
applyxfm = pe.Node(ants.ApplyTransforms(dimension=3, interpolation=interp),
name='FMp_to_B0')
pre_fugue = pe.Node(fsl.FUGUE(save_fmap=True), name='PreliminaryFugue')
demean = pe.Node(niu.Function(input_names=['in_file', 'in_mask'],
output_names=['out_file'],
function=demean_image),
name='DemeanFmap')
cleanup = cleanup_edge_pipeline()
addvol = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_file'],
function=add_empty_vol),
name='AddEmptyVol')
vsm = pe.Node(fsl.FUGUE(save_shift=True, **fugue_params),
name="ComputeVSM")
split = pe.Node(fsl.Split(dimension='t'), name='SplitDWIs')
merge = pe.Node(fsl.Merge(dimension='t'), name='MergeDWIs')
unwarp = pe.MapNode(fsl.FUGUE(icorr=True, forward_warping=False),
iterfield=['in_file'],
name='UnwarpDWIs')
thres = pe.MapNode(fsl.Threshold(thresh=0.0),
iterfield=['in_file'],
name='RemoveNegative')
vsm2dfm = vsm2warp()
vsm2dfm.inputs.inputnode.scaling = 1.0
wf = pe.Workflow(name=name)
wf.connect([(inputnode, r_params, [('settings', 'in_file')]),
(r_params, eff_echo, [('echospacing', 'echospacing'),
('acc_factor', 'acc_factor')]),
(inputnode, pha2rads, [('bmap_pha', 'in_file')]),
(inputnode, firstmag, [('bmap_mag', 'in_file')]),
(inputnode, baseline, [('in_file', 'in_file'),
('in_ref', 'index')]),
(firstmag, n4, [('roi_file', 'input_image')]),
(n4, bet, [('output_image', 'in_file')]),
(bet, dilate, [('mask_file', 'in_file')]),
(pha2rads, prelude, [('out_file', 'phase_file')]),
(n4, prelude, [('output_image', 'magnitude_file')]),
(dilate, prelude, [('out_file', 'mask_file')]),
(r_params, rad2rsec, [('delta_te', 'delta_te')]),
(prelude, rad2rsec, [('unwrapped_phase_file', 'in_file')]),
(baseline, fmm2b0, [('out_file', 'fixed_image')]),
(n4, fmm2b0, [('output_image', 'moving_image')]),
(inputnode, fmm2b0, [('in_mask', 'fixed_image_mask')]),
(dilate, fmm2b0, [('out_file', 'moving_image_mask')]),
(baseline, applyxfm, [('out_file', 'reference_image')]),
(rad2rsec, applyxfm, [('out_file', 'input_image')]),
(fmm2b0, applyxfm, [('forward_transforms', 'transforms'),
('forward_invert_flags',
'invert_transform_flags')]),
(applyxfm, pre_fugue, [('output_image', 'fmap_in_file')]),
(inputnode, pre_fugue, [('in_mask', 'mask_file')]),
(pre_fugue, demean, [('fmap_out_file', 'in_file')]),
(inputnode, demean, [('in_mask', 'in_mask')]),
(demean, cleanup, [('out_file', 'inputnode.in_file')]),
(inputnode, cleanup, [('in_mask', 'inputnode.in_mask')]),
(cleanup, addvol, [('outputnode.out_file', 'in_file')]),
(inputnode, vsm, [('in_mask', 'mask_file')]),
(addvol, vsm, [('out_file', 'fmap_in_file')]),
(r_params, vsm, [('delta_te', 'asym_se_time')]),
(eff_echo, vsm, [('eff_echo', 'dwell_time')]),
(inputnode, split, [('in_file', 'in_file')]),
(split, unwarp, [('out_files', 'in_file')]),
(vsm, unwarp, [('shift_out_file', 'shift_in_file')]),
(r_params, unwarp, [(('enc_dir', _fix_enc_dir),
'unwarp_direction')]),
(unwarp, thres, [('unwarped_file', 'in_file')]),
(thres, merge, [('out_file', 'in_files')]),
(r_params, vsm2dfm, [(('enc_dir',
_fix_enc_dir), 'inputnode.enc_dir')]),
(merge, vsm2dfm, [('merged_file', 'inputnode.in_ref')]),
(vsm, vsm2dfm, [('shift_out_file', 'inputnode.in_vsm')]),
(merge, outputnode, [('merged_file', 'out_file')]),
(vsm, outputnode, [('shift_out_file', 'out_vsm')]),
(vsm2dfm, outputnode, [('outputnode.out_warp', 'out_warp')])])
return wf
