From 3afcd62bd9bfa3ee0b85c4db1c4eb0eacea577a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= Date: Tue, 20 Feb 2024 09:43:14 +0100 Subject: [PATCH 1/5] Update utils.py - Added 'hsvs' option for 5ttgen function --- nipype/interfaces/mrtrix3/utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index 2ec7eba909..93196cc4e5 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -224,13 +224,14 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec): "fsl", "gif", "freesurfer", + "hsvs", argstr="%s", position=-3, mandatory=True, desc="tissue segmentation algorithm", ) in_file = File( - exists=True, argstr="%s", mandatory=True, position=-2, desc="input image" + exists=False, argstr="%s", mandatory=True, position=-2, desc="input image" ) out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image") From 367776d6f27c06d4a80df1ba9b309529fb8fcdb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= Date: Tue, 20 Feb 2024 09:47:05 +0100 Subject: [PATCH 2/5] Update .zenodo.json --- .zenodo.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 4b8ae1f2a6..6e884e7594 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -911,6 +911,11 @@ "name": "Wu, Jianxiao", "orcid": "0000-0002-4866-272X", }, + { + "affiliation": "Lund University", + "name": "Anijärv, Toomas Erik", + "orcid": "0000-0002-3650-4230", + }, ], "keywords": [ "neuroimaging", From c08e17b992c1fa069963f7b7910a7d66aea746ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= Date: Tue, 20 Feb 2024 13:51:11 +0100 Subject: [PATCH 3/5] Update utils.py - Changed '-inverse' parameter location from 1 to 2 (otherwise cannot use together with -linear) --- nipype/interfaces/mrtrix3/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index 93196cc4e5..d0b474a76b 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -823,7 +823,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec): ) invert = traits.Bool( argstr="-inverse", - position=1, + position=2, desc="Invert the specified transform before using it", ) linear_transform = File( From eda649755b4090ebaa959a771829fec1f9db3ba0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= Date: Wed, 28 Feb 2024 09:03:21 +0100 Subject: [PATCH 4/5] Fix generate5tt input --- nipype/interfaces/mrtrix3/utils.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index d0b474a76b..cb6b31ae91 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -11,6 +11,7 @@ traits, TraitedSpec, File, + Directory, InputMultiPath, isdefined, ) @@ -230,8 +231,10 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec): mandatory=True, desc="tissue segmentation algorithm", ) - in_file = File( - exists=False, argstr="%s", mandatory=True, position=-2, desc="input image" + in_file = traits.Either( + File(exists=True), + Directory(exists=True), + argstr="%s", mandatory=True, position=-2, desc="input image / directory" ) out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image") From 7fc44fd9eb7eb80ef01c3253bb2cd72932389d48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Toomas=20Erik=20Anij=C3=A4rv?= Date: Wed, 28 Feb 2024 09:07:45 +0100 Subject: [PATCH 5/5] Remove the -inverse parameter position change --- nipype/interfaces/mrtrix3/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index cb6b31ae91..cecbc6c855 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -826,7 +826,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec): ) invert = traits.Bool( argstr="-inverse", - position=2, + position=1, desc="Invert the specified transform before using it", ) linear_transform = File(