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Merge pull request #915 from juhuntenburg/enh/epi_reg
Enh/epi reg
2 parents 785f6dd + 257565c commit c9b7909

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‎CHANGES

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Next Release
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============
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* ENH: New FSL interface: EpiReg
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* ENH: New Freesurfer interface: Tkregister2 (for conversion of fsl style matrices to freesurfer format)
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* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.
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* ENH: New Freesurfer interface: MRIPretess

‎nipype/interfaces/fsl/__init__.py

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@@ -19,7 +19,7 @@
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Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd)
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from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
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SigLoss, EddyCorrect)
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SigLoss, EddyCorrect, EpiReg)
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from .dti import (BEDPOSTX, DTIFit, ProbTrackX, ProbTrackX2,
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VecReg, ProjThresh, FindTheBiggest, DistanceMap,

‎nipype/interfaces/fsl/epi.py

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@@ -46,7 +46,7 @@ class PrepareFieldmapInputSpec(FSLCommandInputSpec):
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usedefault=True,
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desc=('do not perform sanity checks for image '
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'size/range/dimensions'))
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out_fieldmap = File(argstr='%s', position=5,
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out_fieldmap = File(argstr='%s', position=4,
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desc='output name for prepared fieldmap')
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@@ -534,6 +534,129 @@ def _gen_filename(self, name):
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return self._list_outputs()['out_file']
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return None
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class EpiRegInputSpec(FSLCommandInputSpec):
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epi = File(exists=True, argstr='--epi=%s', mandatory=True,
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position=-4, desc='EPI image')
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t1_head = File(exists=True, argstr='--t1=%s', mandatory=True,
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position=-3, desc='wholehead T1 image')
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t1_brain = File(exists=True, argstr='--t1brain=%s', mandatory=True,
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position=-2, desc='brain extracted T1 image')
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out_base = traits.String(desc='output base name', argstr='--out=%s',
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position=-1)
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fmap = File(exists=True, argstr='--fmap=%s',
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desc='fieldmap image (in rad/s)')
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fmapmag = File(exists=True, argstr='--fmapmag=%s',
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desc='fieldmap magnitude image - wholehead')
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fmapmagbrain = File(exists=True, argstr='--fmapmagbrain=%s',
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desc='fieldmap magnitude image - brain extracted')
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wmseg = File(exists=True, argstr='--wmseg=%s',
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desc='white matter segmentation of T1 image, has to be named \
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like the t1brain and end on _wmseg')
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echospacing = traits.Float(argstr='--echospacing=%f',
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desc='Effective EPI echo spacing \
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(sometimes called dwell time) - in seconds')
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pedir = traits.Enum('x', 'y', 'z', '-x', '-y', '-z', argstr='--pedir=%s',
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desc='phase encoding direction, dir = x/y/z/-x/-y/-z')
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weight_image = File(exists=True, argstr='--weight=%s',
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desc='weighting image (in T1 space)')
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no_fmapreg = traits.Bool(False, argstr='--nofmapreg',
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desc='do not perform registration of fmap to T1 \
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(use if fmap already registered)')
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no_clean = traits.Bool(False, argstr='--noclean',
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desc='do not clean up intermediate files')
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class EpiRegOutputSpec(TraitedSpec):
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out_file = File(exists=True,
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desc='unwarped and coregistered epi input')
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out_1vol = File(exists=True,
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desc='unwarped and coregistered single volume')
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fmap2str_mat = File(exists=True,
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desc='rigid fieldmap-to-structural transform')
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fmap2epi_mat = File(exists=True,
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desc='rigid fieldmap-to-epi transform')
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fmap_epi = File(exists=True, desc='fieldmap in epi space')
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fmap_str = File(exists=True, desc='fieldmap in structural space')
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fmapmag_str = File(exists=True,
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desc='fieldmap magnitude image in structural space')
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epi2str_inv = File(exists=True,
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desc='rigid structural-to-epi transform')
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epi2str_mat = File(exists=True,
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desc='rigid epi-to-structural transform')
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shiftmap = File(exists=True, desc='shiftmap in epi space')
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fullwarp = File(exists=True,
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desc='warpfield to unwarp epi and transform into \
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structural space')
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wmseg = File(exists=True, desc='white matter segmentation used in flirt bbr')
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wmedge = File(exists=True, desc='white matter edges for visualization')
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class EpiReg(FSLCommand):
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"""
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Runs FSL epi_reg script for simultaneous coregistration and fieldmap
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unwarping.
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Examples
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--------
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>>> from nipype.interfaces.fsl import EpiReg
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>>> epireg = EpiReg()
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>>> epireg.inputs.epi='epi.nii'
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>>> epireg.inputs.t1_head='T1.nii'
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>>> epireg.inputs.t1_brain='T1_brain.nii'
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>>> epireg.inputs.out_base='epi2struct'
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>>> epireg.inputs.fmap='fieldmap_phase_fslprepared.nii'
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>>> epireg.inputs.fmapmag='fieldmap_mag.nii'
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>>> epireg.inputs.fmapmagbrain='fieldmap_mag_brain.nii'
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>>> epireg.inputs.echospacing=0.00067
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>>> epireg.inputs.pedir='y'
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>>> epireg.cmdline #doctest: +ELLIPSIS
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'epi_reg --echospacing=0.000670 --fmap=fieldmap_phase_fslprepared.nii \
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--fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --pedir=y \
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--epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
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>>> epireg.run() # doctest: +SKIP
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"""
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_cmd = 'epi_reg'
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input_spec = EpiRegInputSpec
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output_spec = EpiRegOutputSpec
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '.nii.gz')
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outputs['out_1vol'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_1vol.nii.gz')
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outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmap2str.mat')
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outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmaprads2epi.mat')
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outputs['fmap_epi'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
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outputs['fmap_str'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmaprads2str.nii.gz')
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outputs['fmapmag_str'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmap2str.nii.gz')
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outputs['epi2str_inv'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_inv.mat')
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outputs['epi2str_mat'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '.mat')
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outputs['shiftmap'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
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outputs['fullwarp'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_warp.nii.gz')
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outputs['wmedge'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fast_wmedge.nii.gz')
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outputs['wmseg'] = os.path.join(os.getcwd(),
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self.inputs.out_base + '_fast_wmseg.nii.gz')
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return outputs
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#######################################
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# deprecated interfaces
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#######################################

‎nipype/interfaces/fsl/tests/test_auto_EpiReg.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.interfaces.fsl.epi import EpiReg
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def test_EpiReg_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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echospacing=dict(argstr='--echospacing=%f',
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),
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environ=dict(nohash=True,
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usedefault=True,
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),
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epi=dict(argstr='--epi=%s',
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mandatory=True,
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position=-4,
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),
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fmap=dict(argstr='--fmap=%s',
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),
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fmapmag=dict(argstr='--fmapmag=%s',
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),
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fmapmagbrain=dict(argstr='--fmapmagbrain=%s',
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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no_clean=dict(argstr='--noclean',
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),
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no_fmapreg=dict(argstr='--nofmapreg',
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),
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out_base=dict(argstr='--out=%s',
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position=-1,
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),
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output_type=dict(),
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pedir=dict(argstr='--pedir=%s',
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),
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t1_brain=dict(argstr='--t1brain=%s',
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mandatory=True,
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position=-2,
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),
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t1_head=dict(argstr='--t1=%s',
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mandatory=True,
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position=-3,
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),
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terminal_output=dict(mandatory=True,
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nohash=True,
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),
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weight_image=dict(argstr='--weight=%s',
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),
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wmseg=dict(argstr='--wmseg=%s',
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),
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)
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inputs = EpiReg.input_spec()
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for key, metadata in input_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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def test_EpiReg_outputs():
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output_map = dict(epi2str_inv=dict(),
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epi2str_mat=dict(),
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fmap2epi_mat=dict(),
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fmap2str_mat=dict(),
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fmap_epi=dict(),
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fmap_str=dict(),
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fmapmag_str=dict(),
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fullwarp=dict(),
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out_1vol=dict(),
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out_file=dict(),
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shiftmap=dict(),
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wmedge=dict(),
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wmseg=dict(),
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)
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outputs = EpiReg.output_spec()
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for key, metadata in output_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(outputs.traits()[key], metakey), value
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‎nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py

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@@ -29,7 +29,7 @@ def test_PrepareFieldmap_inputs():
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usedefault=True,
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),
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out_fieldmap=dict(argstr='%s',
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position=5,
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position=4,
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),
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output_type=dict(),
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scanner=dict(argstr='%s',

‎nipype/testing/data/T1_brain.nii

Whitespace-only changes.

‎nipype/testing/data/fieldmap_mag.nii

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‎nipype/testing/data/fieldmap_mag_brain.nii

Whitespace-only changes.

‎nipype/testing/data/fieldmap_phase_fslprepared.nii

Whitespace-only changes.

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