ENH: MRIQC for DWI

mriqc/cli/parser.py

@@ -197,6 +197,8 @@ def _bids_filter(value):
         "-m",
         "--modalities",
         action="store",
+        choices=config.SUPPORTED_SUFFIXES,
+        default=config.SUPPORTED_SUFFIXES,
         nargs="*",
         help="Filter input dataset by MRI type.",
     )
@@ -440,7 +442,7 @@ def parse_args(args=None, namespace=None):
     from logging import DEBUG
     from contextlib import suppress
 
-    from ..utils.bids import collect_bids_data
+    from mriqc.utils.bids import collect_bids_data
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
@@ -538,7 +540,7 @@ def parse_args(args=None, namespace=None):
         )
 
     # Check no DWI or others are sneaked into MRIQC
-    unknown_mods = set(config.workflow.inputs.keys()) - set(("T1w", "T2w", "bold"))
+    unknown_mods = set(config.workflow.inputs.keys()) - set(config.SUPPORTED_SUFFIXES)
     if unknown_mods:
         parser.error(
             "MRIQC is unable to process the following modalities: "

mriqc/cli/run.py

@@ -195,14 +195,13 @@ def main():
     # Set up group level
     if "group" in config.workflow.analysis_level:
         from mriqc.reports.group import gen_html as group_html
-        from ..utils.bids import DEFAULT_TYPES
         from ..utils.misc import generate_tsv  # , generate_pred
 
         config.loggers.cli.info(messages.GROUP_START)
 
         # Generate reports
         mod_group_reports = []
-        for mod in config.execution.modalities or DEFAULT_TYPES:
+        for mod in config.execution.modalities or config.SUPPORTED_SUFFIXES:
             output_dir = config.execution.output_dir
             dataframe, out_tsv = generate_tsv(output_dir, mod)
             # If there are no iqm.json files, nothing to do.

mriqc/config.py

@@ -130,6 +130,8 @@
 logging.addLevelName(25, "IMPORTANT")  # Add a new level between INFO and WARNING
 logging.addLevelName(15, "VERBOSE")  # Add a new level between INFO and DEBUG
 
+SUPPORTED_SUFFIXES = ("T1w", "T2w", "bold", "dwi")
+
 DEFAULT_MEMORY_MIN_GB = 0.01
 DSA_MESSAGE = """\
 IMPORTANT: Anonymized quality metrics (IQMs) will be submitted to MRIQC's metrics \
@@ -443,10 +445,10 @@ def init(cls):
                 # Ignore all modality subfolders, except for func/ or anat/
                 re.compile(
                     r"^/sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/"
-                    r"(beh|dwi|fmap|pet|perf|meg|eeg|ieeg|micr|nirs)"
+                    r"(beh|fmap|pet|perf|meg|eeg|ieeg|micr|nirs)"
                 ),
                 # Ignore all files, except for the supported modalities
-                re.compile(r"^.+(?<!(_T1w|_T2w|bold))\.(json|nii|nii\.gz)$"),
+                re.compile(r"^.+(?<!(_T1w|_T2w|bold|_dwi))\.(json|nii|nii\.gz)$"),
             ]
 
             if cls.participant_label:

mriqc/data/bootstrap-dwi.yml

@@ -0,0 +1,77 @@
+# Copyright 2023 The NiPreps Developers <nipreps@gmail.com>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+###########################################################################
+# Reports bootstrap file
+# ======================
+# This is a YAML-formatted file specifying how the NiReports assembler
+# will search for "reportlets" and compose them into a report file,
+# typically in HTML format.
+###########################################################################
+
+packagename: mriqc
+title: '{filename} :: Diffusion MRI MRIQC report'
+sections:
+- name: Summary
+  reportlets:
+  - bids: {datatype: figures, desc: summary, extension: [.html]}
+- name: DWI shells
+  ordering: bval
+  reportlets:
+  - bids: {datatype: figures, desc: zoomedavg}
+    caption: This panel shows a mosaic of the brain. This mosaic is the most suitable to
+      screen head-motion intensity inhomogeneities, global/local noise, signal leakage
+      (for example, from the eyeballs and across the phase-encoding axis), etc.
+    subtitle: Voxel-wise average across volumes in this <em>DWI shell</em>,
+      zoomed-in covering just the brain
+  - bids: {datatype: figures, desc: zoomedstd}
+    caption: This panel shows a mosaic of the brain. This mosaic is the most suitable to
+      screen within-volume head-motion (e.g., missing slices) and reconstruction ghosts
+      such as those intrinsic to SMS parallelization.
+    subtitle: Voxel-wise standard deviation calculated across volumes in this <em>DWI shell</em>,
+      zoomed-in covering just the brain
+  - bids: {datatype: figures, desc: background}
+    caption: This panel shows a mosaic enhancing the background around the head.
+      Artifacts usually unveil themselves in the air surrounding the head, where no signal
+      sources are present.
+    subtitle: View of the background of the voxel-wise average of this <em>DWI shell</em>
+
+- name: About
+  nested: true
+  reportlets:
+  - custom: errors
+    path: '{reportlets_dir}/{run_uuid}'
+    captions: <em>MRIQC</em> may have recorded failure conditions.
+    title: Errors
+  - metadata: "input"
+    settings:
+      # By default, only the first dictionary will be expanded.
+      # If folded is true, all will be folded. If false all expanded.
+      folded: true
+      # If an ID is not provided, one should be generated automatically
+      id: 'about-metadata'
+    caption: |
+      Thanks for using <em>MRIQC</em>. The following information may assist in
+      reconstructing the provenance of the corresponding derivatives.
+    title: Reproducibility and provenance information
+
+# Rating widget
+plugins:
+- module: nireports.assembler
+  path: data/rating-widget/bootstrap.yml

mriqc/data/tests/gh1086-ds004134.oracle

@@ -1 +1 @@
-180
+182