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[FIX] Mrtrix3 usedefault issue #3004

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[FIX] Mrtrix3 usedefault issue #3004

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f490616
Fixed issue with CSD estimation in MRtrix3
matteomancini Aug 19, 2019
4bca4a4
Removing forced optional argument in MRtrix3
matteomancini Aug 19, 2019
9c5dc6e
Fix to make test pass
matteomancini Aug 19, 2019
ba66142
Update nipype/interfaces/mrtrix3/reconst.py
matteomancini Sep 3, 2019
ef40504
Update nipype/interfaces/mrtrix3/reconst.py
matteomancini Sep 3, 2019
be919a5
Update nipype/interfaces/mrtrix3/reconst.py
matteomancini Sep 3, 2019
2c46d9b
Merge remote-tracking branch 'upstream/master' into mrtrix3-usedefaul…
effigies Feb 23, 2020
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7 changes: 3 additions & 4 deletions nipype/interfaces/mrtrix3/reconst.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,10 +102,10 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec):
mandatory=True,
desc='output WM ODF')
gm_txt = File(argstr='%s', position=-4, desc='GM response text file')
gm_odf = File('gm.mif', usedefault=True, argstr='%s',
gm_odf = File('gm.mif', usedefault=False, 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',
csf_odf = File('csf.mif', usedefault=False, argstr='%s',
position=-1, desc='output CSF ODF')
mask_file = File(exists=True, argstr='-mask %s', desc='mask image')

Expand All @@ -118,7 +118,6 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec):
max_sh = InputMultiObject(
traits.Int,
value=[8],
usedefault=True,
argstr='-lmax %s',
sep=',',
desc=('maximum harmonic degree of response function - single value for single-shell response, list for multi-shell response'))
Expand Down Expand Up @@ -151,7 +150,7 @@ class EstimateFOD(MRTrix3Base):
>>> fod.inputs.wm_txt = 'wm.txt'
>>> fod.inputs.grad_fsl = ('bvecs', 'bvals')
>>> fod.cmdline # doctest: +ELLIPSIS
'dwi2fod -fslgrad bvecs bvals -lmax 8 csd dwi.mif wm.txt wm.mif gm.mif csf.mif'
'dwi2fod -fslgrad bvecs bvals csd dwi.mif wm.txt wm.mif'
>>> fod.run() # doctest: +SKIP
"""

Expand Down