Merge pull request #98 from effigies/fix/no_reorient_magnitude

FIX: Do not reorient magnitude images

Author: effigies

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
+templateflow

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),

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