ENH: Add reference_mask script

Author: effigies

Dockerfile

@@ -164,6 +164,10 @@ RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
     pip install .[all] && \
     rm -rf ~/.cache/pip
 
+RUN install -m 0755 \
+    /root/src/fmriprep/scripts/generate_reference_mask.py \
+    /usr/local/bin/generate_reference_mask
+
 RUN ldconfig
 WORKDIR /tmp/
 ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]

scripts/generate_reference_mask.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+import sys
+import os
+from niworkflows.nipype.pipeline import engine as pe
+from niworkflows.nipype.interfaces import utility as niu
+from niworkflows.nipype.utils.filemanip import fname_presuffix, copyfile
+from fmriprep.workflows.bold.utils import init_bold_reference_wf
+
+
+def sink_ref_file(in_file, orig_file, out_dir):
+    out_file = fname_presuffix(orig_file, suffix='_ref', newpath=out_dir)
+    copyfile(in_file, out_file)
+    return out_file
+
+
+def init_main_wf(bold_file, out_dir, base_dir=None, name='main_wf'):
+    wf = init_bold_reference_wf(enhance_t2=True,
+                                base_dir=base_dir,
+                                name=name)
+    wf.inputs.inputnode.bold_file = bold_file
+
+    sink = pe.Node(Function(function=sink_ref_file, out_dir=out_dir,
+                            orig_file=bold_file),
+                   name='sink')
+    wf.connect([
+        ('outputnode', 'sink', [('bold_mask', 'in_file')]),
+        ])
+
+
+def main():
+    main_wf = init_main_wf(sys.argv[1], sys.argv[2])
+    main_wf.run()