From 24ed91a0b4eb09af0135127c2216da29a32a3e4f Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 18 Mar 2020 13:04:01 +1100 Subject: [PATCH 1/4] removed usedefault as it prevents use of WM only CSD algorithm --- .gitignore | 2 ++ nipype/interfaces/mrtrix3/reconst.py | 9 ++++----- 2 files changed, 6 insertions(+), 5 deletions(-) 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..5a9dd2a6d0 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -4,7 +4,8 @@ import os.path as op -from ..base import traits, TraitedSpec, File, Undefined, InputMultiObject +from ..base import ( + traits, TraitedSpec, File, Undefined, InputMultiObject, DynamicTraitedSpec) from .base import MRTrix3BaseInputSpec, MRTrix3Base @@ -109,12 +110,10 @@ 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 From 44e77556b77bebbad6a375e9dd7bdeef7c7011c0 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 18 Mar 2020 13:05:11 +1100 Subject: [PATCH 2/4] removed unrequired import --- nipype/interfaces/mrtrix3/reconst.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 5a9dd2a6d0..62eda89200 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -4,8 +4,7 @@ import os.path as op -from ..base import ( - traits, TraitedSpec, File, Undefined, InputMultiObject, DynamicTraitedSpec) +from ..base import traits, TraitedSpec, File, Undefined, InputMultiObject from .base import MRTrix3BaseInputSpec, MRTrix3Base From 5fdb20555322d2070c5a10ad3c87cdc51b42ff98 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 18 Mar 2020 13:58:58 +1100 Subject: [PATCH 3/4] fixed example to match new behaviour --- nipype/interfaces/mrtrix3/reconst.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 62eda89200..514622e021 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -169,6 +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 From 6ea05042a7705a35f0c3cd7889d68f5a1ccb6a7a Mon Sep 17 00:00:00 2001 From: Tom Close Date: Wed, 18 Mar 2020 15:58:44 +1100 Subject: [PATCH 4/4] removed usedefault from test_EstimateFOD_inputs --- nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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"],),