diff --git a/.gitignore b/.gitignore index 4213d07a68..49dfe1f72f 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,5 @@ __pycache__/ .ipynb_checkpoints/ .ruby-version .pytest_cache +.vscode +.history diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 3f21e9ad54..514622e021 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -109,12 +109,10 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec): ) gm_txt = File(argstr="%s", position=-4, desc="GM response text file") gm_odf = File( - "gm.mif", usedefault=True, argstr="%s", position=-3, desc="output GM ODF" - ) + "gm.mif", argstr="%s", position=-3, desc="output GM ODF") csf_txt = File(argstr="%s", position=-2, desc="CSF response text file") csf_odf = File( - "csf.mif", usedefault=True, argstr="%s", position=-1, desc="output CSF ODF" - ) + "csf.mif", argstr="%s", position=-1, desc="output CSF ODF") mask_file = File(exists=True, argstr="-mask %s", desc="mask image") # DW Shell selection options @@ -171,6 +169,8 @@ class EstimateFOD(MRTrix3Base): >>> fod.inputs.in_file = 'dwi.mif' >>> fod.inputs.wm_txt = 'wm.txt' >>> fod.inputs.grad_fsl = ('bvecs', 'bvals') + >>> fod.inputs.gm_odf = 'gm.mif' + >>> fod.inputs.csf_odf = 'csf.mif' >>> fod.cmdline 'dwi2fod -fslgrad bvecs bvals -lmax 8 msmt_csd dwi.mif wm.txt wm.mif gm.mif csf.mif' >>> fod.run() # doctest: +SKIP diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index bfadae423f..9506f84e4a 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -7,10 +7,10 @@ def test_EstimateFOD_inputs(): algorithm=dict(argstr="%s", mandatory=True, position=-8,), args=dict(argstr="%s",), bval_scale=dict(argstr="-bvalue_scaling %s",), - csf_odf=dict(argstr="%s", extensions=None, position=-1, usedefault=True,), + csf_odf=dict(argstr="%s", extensions=None, position=-1,), csf_txt=dict(argstr="%s", extensions=None, position=-2,), environ=dict(nohash=True, usedefault=True,), - gm_odf=dict(argstr="%s", extensions=None, position=-3, usedefault=True,), + gm_odf=dict(argstr="%s", extensions=None, position=-3,), gm_txt=dict(argstr="%s", extensions=None, position=-4,), grad_file=dict(argstr="-grad %s", extensions=None, xor=["grad_fsl"],), grad_fsl=dict(argstr="-fslgrad %s %s", xor=["grad_file"],),