Merge pull request #49 from eilidhmacnicol/fix/reorder_target_massaging

FIX: reorder pre-brain extraction massaging PIN: pandas and scipy versions in docker file
nipreps · Oct 2, 2021 · e8600b7 · e8600b7
2 parents 526d081 + 1f97483
commit e8600b7
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -78,10 +78,10 @@ RUN conda install -y python=3.7.1 \
                      mkl=2018.0.3 \
                      mkl-service \
                      numpy>=1.16.5 \
-                     scipy=1.1.0 \
+                     scipy=1.2.0 \
                      scikit-learn>=0.20 \
                      matplotlib=2.2.2 \
-                     pandas=0.23.4 \
+                     pandas=0.24 \
                      libxml2=2.9.8 \
                      libxslt=1.1.32 \
                      graphviz=2.40.1 \

diff --git a/nirodents/workflows/brainextraction.py b/nirodents/workflows/brainextraction.py
@@ -183,11 +183,11 @@ def init_rodent_brain_extraction_wf(
     # fmt: off
     wf.connect([
         # Target image massaging
-        (inputnode, clip_target, [(("in_files", _pop), "in_file")]),
+        (inputnode, denoise, [(("in_files", _pop), "input_image")]),
         (inputnode, bspline_grid, [(("in_files", _pop), "in_file")]),
         (bspline_grid, init_n4, [("out", "args")]),
-        (clip_target, denoise, [("out_file", "input_image")]),
-        (denoise, init_n4, [("output_image", "input_image")]),
+        (denoise, clip_target, [("output_image", "in_file")]),
+        (clip_target, init_n4, [("out_file", "input_image")]),
         (init_n4, clip_inu, [("output_image", "in_file")]),
         (clip_inu, target_sigma, [("out_file", "in_file")]),
         (clip_inu, buffernode, [("out_file", "hires_target")]),