From 6e186f9d57290eeb1f5f62faa75a233a7f6d8825 Mon Sep 17 00:00:00 2001 From: GalKepler Date: Mon, 31 Jul 2023 22:59:52 +0300 Subject: [PATCH 1/5] fixed DWIPreproc issue --- nipype/interfaces/mrtrix3/preprocess.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index a097295eea..c2f31fa504 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -406,7 +406,7 @@ class DWIPreproc(MRTrix3Base): def _list_outputs(self): outputs = self.output_spec().get() outputs["out_file"] = op.abspath(self.inputs.out_file) - if self.inputs.export_grad_mrtrix: + if self.inputs.out_grad_mrtrix: outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix) if self.inputs.export_grad_fsl: outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0]) From 60078480705ac673bddba7b757484e67b156aac9 Mon Sep 17 00:00:00 2001 From: GalKepler Date: Mon, 31 Jul 2023 23:02:10 +0300 Subject: [PATCH 2/5] updated my name in zenodo.json --- .zenodo.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.zenodo.json b/.zenodo.json index 807d1c5c4f..4b8ae1f2a6 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -320,7 +320,7 @@ }, { "affiliation": "Sagol School of Neuroscience, Tel Aviv University", - "name": "Ben-Zvi, Gal", + "name": "Kepler, Gal", "orcid": "0000-0002-5655-9423" }, { From f543c4a0c276f5460d1fc50d0d33fb0cc2630b90 Mon Sep 17 00:00:00 2001 From: GalKepler Date: Tue, 1 Aug 2023 00:19:05 +0300 Subject: [PATCH 3/5] noticed that this error also happens for 'out_grad_fsl'. Fixed it --- nipype/interfaces/mrtrix3/preprocess.py | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index c2f31fa504..afedb87749 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -192,7 +192,9 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec): mandatory=True, desc="input DWI image", ) - in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation") + in_mask = File( + argstr="-mask %s", desc="input mask image for bias field estimation" + ) use_ants = traits.Bool( argstr="ants", mandatory=True, @@ -407,8 +409,10 @@ def _list_outputs(self): outputs = self.output_spec().get() outputs["out_file"] = op.abspath(self.inputs.out_file) if self.inputs.out_grad_mrtrix: - outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix) - if self.inputs.export_grad_fsl: + outputs["out_grad_mrtrix"] = op.abspath( + self.inputs.out_grad_mrtrix + ) + if self.inputs.out_fsl_bvec: outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0]) outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1]) @@ -441,9 +445,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec): usedefault=True, desc="output WM response text file", ) - gm_file = File(argstr="%s", position=-2, desc="output GM response text file") - csf_file = File(argstr="%s", position=-1, desc="output CSF response text file") - in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image") + gm_file = File( + argstr="%s", position=-2, desc="output GM response text file" + ) + csf_file = File( + argstr="%s", position=-1, desc="output CSF response text file" + ) + in_mask = File( + exists=True, argstr="-mask %s", desc="provide initial mask image" + ) max_sh = InputMultiObject( traits.Int, argstr="-lmax %s", From 9544f2b69cb45edb0951748461ba434c8e979ff4 Mon Sep 17 00:00:00 2001 From: GalKepler Date: Tue, 1 Aug 2023 00:20:48 +0300 Subject: [PATCH 4/5] fixed type --- nipype/interfaces/mrtrix3/preprocess.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index afedb87749..115cd773bd 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -412,7 +412,7 @@ def _list_outputs(self): outputs["out_grad_mrtrix"] = op.abspath( self.inputs.out_grad_mrtrix ) - if self.inputs.out_fsl_bvec: + if self.inputs.out_grad_fsl: outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0]) outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1]) From 7420058e142224dd2cfaccb84eedbf19b629775e Mon Sep 17 00:00:00 2001 From: GalKepler Date: Tue, 1 Aug 2023 00:24:11 +0300 Subject: [PATCH 5/5] formatted according to nipype's specifications --- nipype/interfaces/mrtrix3/preprocess.py | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index 115cd773bd..d19e13cf69 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -192,9 +192,7 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec): mandatory=True, desc="input DWI image", ) - in_mask = File( - argstr="-mask %s", desc="input mask image for bias field estimation" - ) + in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation") use_ants = traits.Bool( argstr="ants", mandatory=True, @@ -409,9 +407,7 @@ def _list_outputs(self): outputs = self.output_spec().get() outputs["out_file"] = op.abspath(self.inputs.out_file) if self.inputs.out_grad_mrtrix: - outputs["out_grad_mrtrix"] = op.abspath( - self.inputs.out_grad_mrtrix - ) + outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix) if self.inputs.out_grad_fsl: outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0]) outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1]) @@ -445,15 +441,9 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec): usedefault=True, desc="output WM response text file", ) - gm_file = File( - argstr="%s", position=-2, desc="output GM response text file" - ) - csf_file = File( - argstr="%s", position=-1, desc="output CSF response text file" - ) - in_mask = File( - exists=True, argstr="-mask %s", desc="provide initial mask image" - ) + gm_file = File(argstr="%s", position=-2, desc="output GM response text file") + csf_file = File(argstr="%s", position=-1, desc="output CSF response text file") + in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image") max_sh = InputMultiObject( traits.Int, argstr="-lmax %s",