Merge pull request #1299 from poldracklab/fix/enhance_t2

[FIX] Enhance T2 contrast ``enhance_t2`` in reference estimate

Author: oesteban

.circleci/config.yml

@@ -252,10 +252,12 @@ jobs:
           name: Run fMRIPrep tests
           no_output_timeout: 2h
           command: |
+            mkdir /tmp/data/reports && \
             docker run -ti --rm=false \
               -v /tmp/data:/tmp/data \
               -e FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
               -e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
+              -e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ \
               --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
@@ -284,7 +286,7 @@ jobs:
             fmriprep-docker -i poldracklab/fmriprep:latest --help
             fmriprep-docker -i poldracklab/fmriprep:latest --version
       - store_artifacts:
-          path: /home/circleci/out/tests
+          path: /tmp/data/reports
 
 
   build_docs:

fmriprep/workflows/bold/tests/test_util.py

@@ -3,8 +3,12 @@
 import os
 
 import numpy as np
+from nipype.pipeline import engine as pe
 from nipype.utils.filemanip import fname_presuffix
 from nilearn.image import load_img
+
+from niworkflows.interfaces.masks import ROIsPlot
+
 from ..util import init_bold_reference_wf
 
 
@@ -47,6 +51,24 @@ def symmetric_overlap(img1, img2):
 def test_masking(input_fname, expected_fname):
     bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, enhance_t2=True)
     bold_reference_wf.inputs.inputnode.bold_file = input_fname
+
+    # Reconstruct base_fname from above
+    dirname, basename = os.path.split(input_fname)
+    newpath = os.path.join(os.getenv('FMRIPREP_REGRESSION_REPORTS', '.'),
+                           os.path.basename(dirname))
+    out_fname = fname_presuffix(basename, suffix='_masks.svg', use_ext=False,
+                                newpath=newpath)
+    os.makedirs(newpath, exist_ok=True)
+
+    mask_diff_plot = pe.Node(ROIsPlot(), name='mask_diff_plot')
+    mask_diff_plot.inputs.in_mask = expected_fname
+    mask_diff_plot.inputs.out_report = out_fname
+
+    bold_reference_wf.connect([
+        (bold_reference_wf.get_node('outputnode'), mask_diff_plot, [
+            ('ref_image', 'in_file'),
+            ('bold_mask', 'in_rois'),
+            ])])
     res = bold_reference_wf.run(plugin='MultiProc')
 
     combine_masks = [node for node in res.nodes if node.name.endswith('combine_masks')][0]

fmriprep/workflows/bold/util.py

@@ -105,7 +105,8 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, name='bold_reference_wf
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
     # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
     validate_ref = pe.Node(ValidateImage(), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
-    enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
+    enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads,
+                                                                         enhance_t2=enhance_t2)
 
     workflow.connect([
         (inputnode, validate, [('bold_file', 'in_file')]),