MERGE: 1.4.9

Author: mgxd

.circleci/config.yml

@@ -97,9 +97,9 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - env-v1-{{ .Branch }}-
-            - env-v1-master-
-            - env-v1-
+            - env-v2-{{ .Branch }}-
+            - env-v2-master-
+            - env-v2-
       - run:
           name: Setup git-annex, DataLad & TemplateFlow
           command: |
@@ -109,7 +109,7 @@ jobs:
             git config --global user.email 'nipreps@gmail.com'
             python -m pip install --no-cache-dir -U templateflow
       - save_cache:
-          key: env-v1-{{ .Branch }}-{{ .BuildNum }}
+          key: env-v2-{{ .Branch }}-{{ .BuildNum }}
           paths:
             - /opt/conda
 

CHANGES.rst

@@ -54,6 +54,16 @@ This release upgrades the Dockerfile to use FSL6, and includes some new interfac
   * FIX: Scipy docs path (#681)
   * TEST: Drop excessively long interface equivalence tests (#674)
 
+1.4.9 (April 21, 2022)
+======================
+Bug-fix release in the 1.4.x series.
+
+This release includes improvements to the reliability of the BOLD masking workflow,
+as well as an fMRIPrep bug-fix when reusing multi-echo anatomicals.
+
+  * FIX: Account for potential lists of lists in multi-echo cases (#719)
+  * FIX: Improve reliability of BOLD masking workflow (#712)
+
 1.4.8 (April 08, 2022)
 ======================
 Bug-fix release in the 1.4.x series.

niworkflows/func/util.py

@@ -482,8 +482,7 @@ def init_enhance_and_skullstrip_bold_wf(
         norm.inputs.fixed_image = str(bold_template)
         map_brainmask = pe.Node(
             ApplyTransforms(
-                interpolation="BSpline",
-                float=True,
+                interpolation="Linear",
                 # Use the higher resolution and probseg for numerical stability in rounding
                 input_image=str(
                     get_template(
@@ -523,7 +522,7 @@ def init_enhance_and_skullstrip_bold_wf(
     workflow.connect([
         (inputnode, check_hdr, [("in_file", "reference")]),
         (pre_dilate, check_hdr, [("out_file", "in_file")]),
-        (check_hdr, n4_correct, [("out_file", "mask_image")]),
+        (check_hdr, n4_correct, [("out_file", "weight_image")]),
         (inputnode, n4_correct, [("in_file", "input_image")]),
         (inputnode, fixhdr_unifize, [("in_file", "hdr_file")]),
         (inputnode, fixhdr_skullstrip2, [("in_file", "hdr_file")]),

niworkflows/utils/misc.py

@@ -107,11 +107,20 @@ def fix_multi_T1w_source_name(in_files):
     ...     '/path/to/sub-045_ses-retest_T1w.nii.gz'])
     '/path/to/sub-045_T1w.nii.gz'
 
+
+    >>> fix_multi_T1w_source_name([
+    ...    ('/path/to/sub-045-echo-1_T1w.nii.gz', 'path/to/sub-045-echo-2_T1w.nii.gz')])
+    '/path/to/sub-045_T1w.nii.gz'
+
     """
     import os
     from nipype.utils.filemanip import filename_to_list
 
-    base, in_file = os.path.split(filename_to_list(in_files)[0])
+    in_file = filename_to_list(in_files)[0]
+    if isinstance(in_file, (list, tuple)):
+        in_file = in_file[0]
+
+    base, in_file = os.path.split(in_file)
     subject_label = in_file.split("_", 1)[0].split("-")[1]
     return os.path.join(base, "sub-%s_T1w.nii.gz" % subject_label)