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Adam Richie-Halford
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Add EddyQuad interface
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‎nipype/interfaces/fsl/__init__.py‎

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@@ -21,7 +21,7 @@
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WarpPointsFromStd, RobustFOV, CopyGeom, MotionOutliers)
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from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp, SigLoss,
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EddyCorrect, EpiReg)
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EddyCorrect, EpiReg, EddyQuad)
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from .dti import (BEDPOSTX, XFibres, DTIFit, ProbTrackX, ProbTrackX2, VecReg,
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ProjThresh, FindTheBiggest, DistanceMap, TractSkeleton,
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MakeDyadicVectors, BEDPOSTX5, XFibres5)

‎nipype/interfaces/fsl/epi.py‎

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@@ -1232,3 +1232,217 @@ def _run_interface(self, runtime):
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if runtime.stderr:
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self.raise_exception(runtime)
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return runtime
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class EddyQuadInputSpec(FSLCommandInputSpec):
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base_name = traits.Str(
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'eddy_corrected',
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argstr='%s',
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desc="Basename (including path) specified when running EDDY",
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position=0,
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)
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idx_file = File(
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exists=True,
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mandatory=True,
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argstr="--eddyIdx=%s",
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desc=("File containing indices for all volumes into acquisition "
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"parameters")
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)
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param_file = File(
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exists=True,
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mandatory=True,
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argstr="--eddyParams=%s",
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desc="File containing acquisition parameters"
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)
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mask_file = File(
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exists=True,
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mandatory=True,
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argstr="--mask=%s",
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desc="Binary mask file"
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)
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bval_file = File(
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exists=True,
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mandatory=True,
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argstr="--bvals=%s",
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desc="b-values file"
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)
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bvec_file = File(
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exists=True,
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mandatory=False,
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argstr="--bvecs=%s",
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desc=("b-vectors file - only used when <base_name>.eddy_residuals "
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"file is present")
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)
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output_dir = traits.Str(
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'eddy_corrected.qc',
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mandatory=False,
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argstr='--output-dir=%s',
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desc="Output directory - default = '<base_name>.qc'",
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)
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field = File(
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mandatory=False,
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argstr='--field=%s',
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desc="TOPUP estimated field (in Hz)",
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)
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slspec = File(
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mandatory=False,
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argstr='--slspec=%s',
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desc="Text file specifying slice/group acquisition",
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)
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verbose = traits.Bool(
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False,
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mandatory=False,
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argstr='--verbose',
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desc="Display debug messages",
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)
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class EddyQuadOutputSpec(TraitedSpec):
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out_qc_json = File(
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exists=True,
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mandatory=True,
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desc=("Single subject database containing quality metrics and data "
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"info.")
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)
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out_qc_pdf = File(
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exists=True,
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mandatory=True,
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desc="Single subject QC report."
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)
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out_avg_b_png = traits.List(
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File(
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exists=True,
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mandatory=True,
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desc=("Image showing mid-sagittal, -coronal and -axial slices of "
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"each averaged b-shell volume.")
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)
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)
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out_avg_b0_png = traits.List(
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File(
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exists=True,
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mandatory=False,
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desc=("Image showing mid-sagittal, -coronal and -axial slices of "
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"each averaged pe-direction b0 volume. Generated when using "
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"the -f option.")
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)
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)
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out_cnr_png = traits.List(
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File(
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exists=True,
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mandatory=False,
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desc=("Image showing mid-sagittal, -coronal and -axial slices of "
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"each b-shell CNR volume. Generated when CNR maps are "
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"available.")
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)
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)
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out_vdm_png = File(
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exists=True,
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mandatory=False,
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desc=("Image showing mid-sagittal, -coronal and -axial slices of "
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"the voxel displacement map. Generated when using the -f "
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"option.")
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)
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out_residuals = File(
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exists=True,
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mandatory=False,
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desc=("Text file containing the volume-wise mask-averaged squared "
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"residuals. Generated when residual maps are available.")
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)
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out_clean_volumes = File(
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exists=True,
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mandatory=False,
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desc=("Text file containing a list of clean volumes, based on "
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"the eddy squared residuals. To generate a version of the "
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"pre-processed dataset without outlier volumes, use: "
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"`fslselectvols -i <eddy_corrected_data> -o "
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"eddy_corrected_data_clean --vols=vols_no_outliers.txt`")
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)
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class EddyQuad(FSLCommand):
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"""
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Interface for FSL eddy_quad, a tool for generating single subject reports
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and storing the quality assessment indices for each subject.
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`User guide <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddyqc/UsersGuide>`_
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Examples
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--------
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>>> from nipype.interfaces.fsl import EddyQuad
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>>> quad = EddyQuad()
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>>> quad.inputs.in_file = 'epi.nii'
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>>> quad.inputs.in_mask = 'epi_mask.nii'
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>>> quad.inputs.in_index = 'epi_index.txt'
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>>> quad.inputs.in_acqp = 'epi_acqp.txt'
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>>> quad.inputs.in_bvec = 'bvecs.scheme'
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>>> quad.inputs.in_bval = 'bvals.scheme'
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>>> quad.inputs.use_cuda = True
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>>> quad.cmdline # doctest: +ELLIPSIS
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'eddy_cuda --ff=10.0 --acqp=epi_acqp.txt --bvals=bvals.scheme \
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--bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
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--mask=epi_mask.nii --niter=5 --nvoxhp=1000 --out=.../eddy_corrected'
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>>> quad.cmdline # doctest: +ELLIPSIS
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'eddy_openmp --ff=10.0 --acqp=epi_acqp.txt --bvals=bvals.scheme \
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--bvecs=bvecs.scheme --imain=epi.nii --index=epi_index.txt \
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--mask=epi_mask.nii --niter=5 --nvoxhp=1000 --out=.../eddy_corrected'
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>>> res = quad.run() # doctest: +SKIP
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"""
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_cmd = 'eddy_quad'
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input_spec = EddyQuadInputSpec
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output_spec = EddyQuadOutputSpec
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def __init__(self, **inputs):
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super(EddyQuad, self).__init__(**inputs)
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def _list_outputs(self):
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outputs = self.output_spec().get()
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out_dir = self.inputs.output_dir
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outputs['out_qc_json'] = os.path.abspath(
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os.path.join(self.inputs.output_dir, 'out.json')
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)
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outputs['out_qc_json'] = os.path.abspath(
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os.path.join(self.inputs.output_dir, 'out.json')
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)
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outputs['out_parameter'] = os.path.abspath(
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'%s.eddy_parameters' % self.inputs.out_base)
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# File generation might depend on the version of EDDY
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out_rotated_bvecs = os.path.abspath(
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'%s.eddy_rotated_bvecs' % self.inputs.out_base)
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out_movement_rms = os.path.abspath(
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'%s.eddy_movement_rms' % self.inputs.out_base)
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out_restricted_movement_rms = os.path.abspath(
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'%s.eddy_restricted_movement_rms' % self.inputs.out_base)
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out_shell_alignment_parameters = os.path.abspath(
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'%s.eddy_post_eddy_shell_alignment_parameters' %
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self.inputs.out_base)
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out_outlier_report = os.path.abspath(
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'%s.eddy_outlier_report' % self.inputs.out_base)
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if isdefined(self.inputs.cnr_maps) and self.inputs.cnr_maps:
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out_cnr_maps = os.path.abspath(
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'%s.eddy_cnr_maps.nii.gz' % self.inputs.out_base)
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if os.path.exists(out_cnr_maps):
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outputs['out_cnr_maps'] = out_cnr_maps
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if isdefined(self.inputs.residuals) and self.inputs.residuals:
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out_residuals = os.path.abspath(
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'%s.eddy_residuals.nii.gz' % self.inputs.out_base)
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if os.path.exists(out_residuals):
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outputs['out_residuals'] = out_residuals
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if os.path.exists(out_rotated_bvecs):
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outputs['out_rotated_bvecs'] = out_rotated_bvecs
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if os.path.exists(out_movement_rms):
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outputs['out_movement_rms'] = out_movement_rms
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if os.path.exists(out_restricted_movement_rms):
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outputs['out_restricted_movement_rms'] = \
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out_restricted_movement_rms
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if os.path.exists(out_shell_alignment_parameters):
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outputs['out_shell_alignment_parameters'] = \
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out_shell_alignment_parameters
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if os.path.exists(out_outlier_report):
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outputs['out_outlier_report'] = out_outlier_report
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return outputs
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