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Add hidden DOF (and --fsl-dof) options to BBRegister #1917

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Merged
merged 2 commits into from
Apr 1, 2017
Merged

Add hidden DOF (and --fsl-dof) options to BBRegister #1917

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8b4b423
Add hidden DOF options for BBRegister
effigies Mar 16, 2017
2afece9
Update test_BBRegister_inputs
effigies Mar 16, 2017
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9 changes: 6 additions & 3 deletions nipype/interfaces/freesurfer/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1028,6 +1028,10 @@ class BBRegisterInputSpec(FSTraitedSpec):
desc="force use of nifti rather than analyze with SPM")
epi_mask = traits.Bool(argstr="--epi-mask",
desc="mask out B0 regions in stages 1 and 2")
dof = traits.Enum(6, 9, 12, argstr='--%d',
desc='number of transform degrees of freedom')
fsldof = traits.Int(argstr='--fsl-dof %d',
desc='degrees of freedom for initial registration (FSL)')
out_fsl_file = traits.Either(traits.Bool, File, argstr="--fslmat %s",
desc="write the transformation matrix in FSL FLIRT format")
registered_file = traits.Either(traits.Bool, File, argstr='--o %s',
Expand All @@ -1054,9 +1058,8 @@ class BBRegister(FSCommand):
"""Use FreeSurfer bbregister to register a volume to the Freesurfer anatomical.

This program performs within-subject, cross-modal registration using a
boundary-based cost function. The registration is constrained to be 6
DOF (rigid). It is required that you have an anatomical scan of the
subject that has already been recon-all-ed using freesurfer.
boundary-based cost function. It is required that you have an anatomical
scan of the subject that has already been recon-all-ed using freesurfer.

Examples
--------
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4 changes: 4 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_BBRegister.py
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Expand Up @@ -6,8 +6,10 @@ def test_BBRegister_inputs():
input_map_5_3 = dict(
args=dict(argstr='%s',),
contrast_type=dict(argstr='--%s', mandatory=True,),
dof=dict(argstr='--%d',),
environ=dict(nohash=True, usedefault=True,),
epi_mask=dict(argstr='--epi-mask',),
fsldof=dict(argstr='--fsl-dof %d',),
ignore_exception=dict(nohash=True, usedefault=True,),
init=dict(argstr='--init-%s', mandatory=True, xor=['init_reg_file'],),
init_reg_file=dict(argstr='--init-reg %s', mandatory=True, xor=['init'],),
Expand All @@ -26,8 +28,10 @@ def test_BBRegister_inputs():
input_map_6_0 = dict(
args=dict(argstr='%s',),
contrast_type=dict(argstr='--%s', mandatory=True,),
dof=dict(argstr='--%d',),
environ=dict(nohash=True, usedefault=True,),
epi_mask=dict(argstr='--epi-mask',),
fsldof=dict(argstr='--fsl-dof %d',),
ignore_exception=dict(nohash=True, usedefault=True,),
init=dict(argstr='--init-%s', xor=['init_reg_file'],),
init_reg_file=dict(argstr='--init-reg %s', xor=['init'],),
Expand Down