From f4906165bd65ddbf87cfac02fd24fced6d4509ce Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Mon, 19 Aug 2019 15:13:50 -0400 Subject: [PATCH 1/6] Fixed issue with CSD estimation in MRtrix3 --- nipype/interfaces/mrtrix3/reconst.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 4e2db8de3f..5dede1244a 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -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') From 4bca4a44614d11663659e6b81508932b693cb8b8 Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Mon, 19 Aug 2019 15:22:11 -0400 Subject: [PATCH 2/6] Removing forced optional argument in MRtrix3 --- nipype/interfaces/mrtrix3/reconst.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 5dede1244a..cdb0dd0a46 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -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')) From 9c5dc6ec2efb80a6fe834aadb8cafa557029ee68 Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Mon, 19 Aug 2019 16:15:46 -0400 Subject: [PATCH 3/6] Fix to make test pass --- nipype/interfaces/mrtrix3/reconst.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index cdb0dd0a46..6deb4c22b8 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -150,7 +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 """ From ba66142b92d973458f8da21ec69b0fd3ddb26bd0 Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Tue, 3 Sep 2019 11:36:41 -0400 Subject: [PATCH 4/6] Update nipype/interfaces/mrtrix3/reconst.py Co-Authored-By: Chris Markiewicz --- nipype/interfaces/mrtrix3/reconst.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 6deb4c22b8..55c2a82a30 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -117,7 +117,6 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec): desc='specify one or more dw gradient shells') max_sh = InputMultiObject( traits.Int, - value=[8], argstr='-lmax %s', sep=',', desc=('maximum harmonic degree of response function - single value for single-shell response, list for multi-shell response')) From ef4050476ee00cb80f9c5ed635f1d3baba0d2841 Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Tue, 3 Sep 2019 11:36:59 -0400 Subject: [PATCH 5/6] Update nipype/interfaces/mrtrix3/reconst.py Co-Authored-By: Chris Markiewicz --- nipype/interfaces/mrtrix3/reconst.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 55c2a82a30..a87bc9aab0 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -105,7 +105,7 @@ class EstimateFODInputSpec(MRTrix3BaseInputSpec): 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=False, argstr='%s', + csf_odf = File(argstr='%s', position=-1, desc='output CSF ODF') mask_file = File(exists=True, argstr='-mask %s', desc='mask image') From be919a58c9e09031ba12b3a9441e4d3c2806266e Mon Sep 17 00:00:00 2001 From: Matteo Mancini Date: Tue, 3 Sep 2019 11:37:08 -0400 Subject: [PATCH 6/6] Update nipype/interfaces/mrtrix3/reconst.py Co-Authored-By: Chris Markiewicz --- nipype/interfaces/mrtrix3/reconst.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index a87bc9aab0..6487e61d38 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -102,7 +102,7 @@ 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=False, argstr='%s', + gm_odf = File(argstr='%s', position=-3, desc='output GM ODF') csf_txt = File(argstr='%s', position=-2, desc='CSF response text file') csf_odf = File(argstr='%s',