From fc4009bf66fbb74c5b6e4f7996f89c0c1f874983 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Wed, 15 Apr 2020 14:54:53 -0400 Subject: [PATCH 1/2] FIX: Do not reorient magnitude images --- sdcflows/workflows/gre.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sdcflows/workflows/gre.py b/sdcflows/workflows/gre.py index 5615c42ae7..ac11370d4d 100644 --- a/sdcflows/workflows/gre.py +++ b/sdcflows/workflows/gre.py @@ -65,7 +65,8 @@ def init_magnitude_wf(omp_nthreads, name='magnitude_wf'): name='outputnode') # Merge input magnitude images - magmrg = pe.Node(IntraModalMerge(hmc=False), name='magmrg') + # Do not reorient to RAS to preserve the validity of PhaseEncodingDirection + magmrg = pe.Node(IntraModalMerge(hmc=False, to_ras=False), name='magmrg') # de-gradient the fields ("bias/illumination artifact") n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True), From c15234e840c38338b838c333cfd3fe0183caa806 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Wed, 15 Apr 2020 15:06:54 -0400 Subject: [PATCH 2/2] DOC: Require Sphinx <3 --- docs/requirements.txt | 4 ++-- setup.cfg | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 0f9ac31c89..986890d30a 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -8,7 +8,7 @@ packaging pydot>=1.2.3 pydotplus sphinx-argparse -sphinx>=2.1.2 +sphinx>=2.1.2,<3 sphinx_rtd_theme sphinxcontrib-apidoc ~= 0.3.0 -templateflow \ No newline at end of file +templateflow diff --git a/setup.cfg b/setup.cfg index b93f3f2bbe..111dba4fe0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -42,7 +42,7 @@ include_package_data = True [options.extras_require] doc = - sphinx >= 2.1.2 + sphinx >= 2.1.2, <3 pydot >= 1.2.3 pydotplus sphinx_rtd_theme