WIP: PETQC implementation

README.rst

@@ -29,6 +29,14 @@ software engineering principles:
    Its reliability is permanently checked and maintained with
    `CircleCI <https://circleci.com/gh/nipreps/mriqc>`_.
 
+PETQC support
+-------------
+*MRIQC* also provides workflows for quality control of positron emission
+tomography (PET) images. When PET data are detected in a BIDS dataset,
+the PETQC pipeline runs automatically and generates PET-specific IQMs and
+HTML reports. Further details can be found in the
+`documentation <https://mriqc.readthedocs.io/en/latest/petqc.html>`__.
+
 Citation
 --------
 .. topic:: **When using MRIQC, please include the following citation:**

docs/source/index.rst

@@ -18,6 +18,7 @@ Contents
    measures
    reports
    workflows
+   petqc
    dsa
    license
    changes

docs/source/petqc.rst

@@ -0,0 +1,27 @@
+.. _petqc:
+
+PETQC workflows
+***************
+
+MRIQC includes experimental support for positron emission tomography (PET) quality
+control. When PET data are present in a BIDS dataset, the ``pet`` workflow is
+initialized automatically and generates PET-specific image quality metrics.
+
+Running PETQC
+-------------
+
+Executing PETQC does not require additional command line options beyond the
+standard *MRIQC* interface. Simply run::
+
+  mriqc <bids_root> <output_dir> participant
+
+MRIQC will detect ``pet`` images and process them along with other modalities.
+
+Interpreting PETQC outputs
+--------------------------
+
+Individual HTML reports for each PET run are written to
+``<output_dir>/reports``. Summary metrics are collated in
+``<output_dir>/pet.csv`` and a group report is produced when the ``group`` level
+is executed. These outputs mirror those of the MRI workflows and can be used to
+identify artifacts or outlier scans.

mriqc/config.py

@@ -139,7 +139,7 @@
     os.environ['PYTHONWARNINGS'] = 'ignore'
 
 
-SUPPORTED_SUFFIXES: tuple[str, ...] = ('T1w', 'T2w', 'bold', 'dwi')
+SUPPORTED_SUFFIXES: tuple[str, ...] = ('T1w', 'T2w', 'bold', 'dwi', 'pet')
 
 DEFAULT_MEMORY_MIN_GB: float = 0.01
 DSA_MESSAGE: str = """\
@@ -510,10 +510,10 @@ def init(cls) -> None:
                 # Ignore all modality subfolders, except for func/ or anat/
                 re.compile(
                     r'^/sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/'
-                    r'(beh|fmap|pet|perf|meg|eeg|ieeg|micr|nirs)'
+                    r'(beh|fmap|perf|meg|eeg|ieeg|micr|nirs)'
                 ),
                 # Ignore all files, except for the supported modalities
-                re.compile(r'^.+(?<!(_T1w|_T2w|bold|_dwi))\.(json|nii|nii\.gz)$'),
+                re.compile(r'^.+(?<!(_T1w|_T2w|bold|_pet|_dwi))\.(json|nii|nii\.gz)$'),
             ]
 
             if cls.participant_label:

mriqc/data/atlas/petref-mni_registration_precise_000.json

@@ -0,0 +1,24 @@
+{
+    "collapse_output_transforms": true,
+    "convergence_threshold": [1e-6, 1e-6, 1e-6],
+    "convergence_window_size": [20, 20, 10],
+    "dimension": 3,
+    "interpolation": "Linear",
+    "metric": ["Mattes", "Mattes", "Mattes"],
+    "metric_weight": [1, 1, 1],
+    "number_of_iterations": [[1000, 500, 250], [500, 250, 100], [100, 50, 30]],
+    "output_transform_prefix": "pet_to_mni",
+    "output_warped_image": true,
+    "radius_or_number_of_bins": [32, 32, 32],
+    "sampling_percentage": [0.5, 0.5, 1.0],
+    "sampling_strategy": ["Regular", "Regular", "None"],
+    "shrink_factors": [[4, 2, 1], [4, 2, 1], [4, 2, 1]],
+    "sigma_units": ["vox", "vox", "vox"],
+    "smoothing_sigmas": [[6, 3, 1], [4, 2, 1], [2, 1, 0]],
+    "transform_parameters": [[0.1], [0.1], [0.1, 3.0, 0.0]],
+    "transforms": ["Rigid", "Affine", "SyN"],
+    "use_histogram_matching": [true, true, true],
+    "winsorize_lower_quantile": 0.01,
+    "winsorize_upper_quantile": 0.99,
+    "write_composite_transform": false
+}

mriqc/data/atlas/tpl-SPM_space-MNI152_dseg.tsv

@@ -0,0 +1,96 @@
+index	name
+1	TL_hippocampus_R
+2	TL_hippocampus_L
+3	TL_amygdala_R
+4	TL_amygdala_L
+5	TL_anterior_temporal_lobe_medial_part_R
+6	TL_anterior_temporal_lobe_medial_part_L
+7	TL_anterior_temporal_lobe_lateral_part_R
+8	TL_anterior_temporal_lobe_lateral_part_L
+9	TL_parahippocampal_and_ambient_gyrus_R
+10	TL_parahippocampal_and_ambient_gyrus_L
+11	TL_superior_temporal_gyrus_middle_part_R
+12	TL_superior_temporal_gyrus_middle_part_L
+13	TL_middle_and_inferior_temporal_gyrus_R
+14	TL_middle_and_inferior_temporal_gyrus_L
+15	TL_fusiform_gyrus_R
+16	TL_fusiform_gyrus_L
+17	cerebellum_R
+18	cerebellum_L
+19	brainstem_excluding_substantia_nigra
+20	insula_posterior_long_gyrus_L
+21	insula_posterior_long_gyrus_R
+22	OL_lateral_remainder_occipital_lobe_L
+23	OL_lateral_remainder_occipital_lobe_R
+24	CG_anterior_cingulate_gyrus_L
+25	CG_anterior_cingulate_gyrus_R
+26	CG_posterior_cingulate_gyrus_L
+27	CG_posterior_cingulate_gyrus_R
+28	FL_middle_frontal_gyrus_L
+29	FL_middle_frontal_gyrus_R
+30	TL_posterior_temporal_lobe_L
+31	TL_posterior_temporal_lobe_R
+32	PL_angular_gyrus_L
+33	PL_angular_gyrus_R
+34	caudate_nucleus_L
+35	caudate_nucleus_R
+36	nucleus_accumbens_L
+37	nucleus_accumbens_R
+38	putamen_L
+39	putamen_R
+40	thalamus_L
+41	thalamus_R
+42	pallidum_L
+43	pallidum_R
+44	corpus_callosum
+45	Lateral_ventricle_excluding_temporal_horn_R
+46	Lateral_ventricle_excluding_temporal_horn_L
+47	Lateral_ventricle_temporal_horn_R
+48	Lateral_ventricle_temporal_horn_L
+49	Third_ventricle
+50	FL_precentral_gyrus_L
+51	FL_precentral_gyrus_R
+52	FL_straight_gyrus_L
+53	FL_straight_gyrus_R
+54	FL_anterior_orbital_gyrus_L
+55	FL_anterior_orbital_gyrus_R
+56	FL_inferior_frontal_gyrus_L
+57	FL_inferior_frontal_gyrus_R
+58	FL_superior_frontal_gyrus_L
+59	FL_superior_frontal_gyrus_R
+60	PL_postcentral_gyrus_L
+61	PL_postcentral_gyrus_R
+62	PL_superior_parietal_gyrus_L
+63	PL_superior_parietal_gyrus_R
+64	OL_lingual_gyrus_L
+65	OL_lingual_gyrus_R
+66	OL_cuneus_L
+67	OL_cuneus_R
+68	FL_medial_orbital_gyrus_L
+69	FL_medial_orbital_gyrus_R
+70	FL_lateral_orbital_gyrus_L
+71	FL_lateral_orbital_gyrus_R
+72	FL_posterior_orbital_gyrus_L
+73	FL_posterior_orbital_gyrus_R
+74	substantia_nigra_L
+75	substantia_nigra_R
+76	FL_subgenual_frontal_cortex_L
+77	FL_subgenual_frontal_cortex_R
+78	FL_subcallosal_area_L
+79	FL_subcallosal_area_R
+80	FL_pre-subgenual_frontal_cortex_L
+81	FL_pre-subgenual_frontal_cortex_R
+82	TL_superior_temporal_gyrus_anterior_part_L
+83	TL_superior_temporal_gyrus_anterior_part_R
+84	PL_supramarginal_gyrus_L
+85	PL_supramarginal_gyrus_R
+86	insula_anterior_short_gyrus_L
+87	insula_anterior_short_gyrus_R
+88	insula_middle_short_gyrus_L
+89	insula_middle_short_gyrus_R
+90	insula_posterior_short_gyrus_L
+91	insula_posterior_short_gyrus_R
+92	insula_anterior_inferior_cortex_L
+93	insula_anterior_inferior_cortex_R
+94	insula_anterior_long_gyrus_L
+95	insula_anterior_long_gyrus_R

mriqc/data/bootstrap-pet.yml

@@ -0,0 +1,118 @@
+package: mriqc
+title: "{filename} :: MRIQC's PET report"
+sections:
+  - name: Summary
+    reportlets:
+      - bids:
+          datatype: figures
+          desc: summary
+          suffix: pet
+          extension: [.html]
+
+  - name: Motion Correction Reports
+    reportlets:
+      - bids:
+          datatype: figures
+          desc: fd
+          extension: [.png]
+        caption: Framewise Displacement.
+        subtitle: FD
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: rotation
+          extension: [.png]
+        caption: Rotation components of motion correction.
+        subtitle: Rotation Metrics
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: translation
+          extension: [.png]
+        caption: Translation components of motion correction.
+        subtitle: Translation Metrics
+        style:
+          max-width: 800px
+
+  - name: Normalization Report
+    reportlets:
+      - bids:
+          datatype: figures
+          desc: norm
+          extension: [.svg]
+        caption: Spatial normalization to standard (MNI) space. The visualization dynamically transitions between subject PET and template images.
+        subtitle: Normalization Report
+        static: false
+        style:
+          max-width: 800px
+
+  - name: Time-Activity Curves (TACs)
+    reportlets:
+      - bids:
+          datatype: figures
+          desc: tacsCortical
+          extension: [.png]
+        caption: Cortical regions TACs.
+        subtitle: Cortical TACs
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: tacsSubcortical
+          extension: [.png]
+        caption: Subcortical regions TACs.
+        subtitle: Subcortical TACs
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: tacsVentricular
+          extension: [.png]
+        caption: Ventricular regions TACs.
+        subtitle: Ventricular TACs
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: tacsOther
+          extension: [.png]
+        caption: Other regions TACs.
+        subtitle: Other TACs
+        style:
+          max-width: 800px
+
+      - bids:
+          datatype: figures
+          desc: carpet
+          extension: [.svg]
+        caption: Carpet plots of the time-activity curves
+        subtitle: Carpet Plots
+        style:
+          max-width: 800px
+
+  - 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:
+          folded: true
+          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
+
+plugins:
+  - module: nireports.assembler
+    path: data/rating-widget/bootstrap.yml