nipreps · celprov · Apr 30, 2025 · Apr 30, 2025 · May 1, 2025 · May 1, 2025
diff --git a/mriqc/config.py b/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:

diff --git a/mriqc/data/bootstrap-pet.yml b/mriqc/data/bootstrap-pet.yml
@@ -0,0 +1,39 @@
+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: 600px
+
+      - bids:
+          datatype: figures
+          desc: rotation
+          extension: [.png]
+        caption: Rotation components of motion correction.
+        subtitle: Rotation Metrics
+        style:
+          max-width: 600px
+
+      - bids:
+          datatype: figures
+          desc: translation
+          extension: [.png]
+        caption: Translation components of motion correction.
+        subtitle: Translation Metrics
+        style:
+          max-width: 600px
diff --git a/mriqc/data/pet/dataset_description.json b/mriqc/data/pet/dataset_description.json
@@ -0,0 +1,11 @@
+{
+    "Name": "PETPrep HMC workflow",
+    "DatasetType": "derivative",
+    "BIDSVersion": "1.7.0",
+    "GeneratedBy": [
+        {
+            "Name": "petprep_hmc",
+            "Version": "0.0.10"
+        }
+    ]
+}
diff --git a/mriqc/data/pet/derivatives/mriqc/.bids_db/layout_index.sqlite b/mriqc/data/pet/derivatives/mriqc/.bids_db/layout_index.sqlite
diff --git a/...t/derivatives/mriqc/logs/config-20250509-150839_62d91c5f-fc2a-4ed5-87b2-8c474d5e033e.toml b/...t/derivatives/mriqc/logs/config-20250509-150839_62d91c5f-fc2a-4ed5-87b2-8c474d5e033e.toml
@@ -0,0 +1,81 @@
+[environment]
+cache_path = "PosixPath('/Users/martinnorgaard/.cache/mriqc')"
+cpu_count = 10
+exec_env = "posix"
+freesurfer_home = "/Applications/freesurfer/7.4.1"
+overcommit_policy = "n/a"
+overcommit_limit = "n/a"
+nipype_version = "1.10.0"
+synthstrip_path = "PosixPath('/Applications/freesurfer/7.4.1/models/synthstrip.1.pt')"
+templateflow_version = "24.2.2"
+total_memory = 32.0
+version = "25.1.0.dev49+g1b92a165.d20250509"
+
+[execution]
+ants_float = false
+bids_dir = "/Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet"
+bids_dir_datalad = false
+bids_database_dir = "/Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet/derivatives/mriqc/.bids_db"
+bids_database_wipe = false
+cwd = "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/mriqc"
+datalad_get = true
+debug = false
+dry_run = false
+dsname = "<unset>"
+float32 = true
+layout = "BIDS Layout: /Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet"
+log_dir = "/Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet/derivatives/mriqc/logs"
+log_level = 25
+modalities = [ "T1w", "T2w", "bold", "dwi", "pet",]
+no_sub = true
+notrack = false
+output_dir = "/Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet/derivatives/mriqc"
+participant_label = [ "01",]
+pdb = false
+reports_only = false
+resource_monitor = false
+run_uuid = "20250509-150839_62d91c5f-fc2a-4ed5-87b2-8c474d5e033e"
+templateflow_home = "/Users/martinnorgaard/.cache/templateflow"
+upload_strict = false
+verbose_reports = false
+webapi_url = "https://mriqc.nimh.nih.gov:443/api/v1"
+work_dir = "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/mriqc/work"
+write_graph = false
+
+[workflow]
+analysis_level = [ "participant",]
+deoblique = false
+despike = false
+fd_thres = 0.2
+fd_radius = 50
+fft_spikes_detector = false
+inputs_path = "PosixPath('/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/mriqc/work/inputs-20250509-150839_62d91c5f-fc2a-4ed5-87b2-8c474d5e033e.pkl')"
+min_len_dwi = 7
+min_len_bold = 5
+species = "human"
+template_id = "MNI152NLin2009cAsym"
+
+[nipype]
+crashfile_format = "txt"
+get_linked_libs = false
+local_hash_check = true
+nprocs = 10
+omp_nthreads = 10
+plugin = "MultiProc"
+remove_node_directories = false
+resource_monitor = false
+stop_on_first_crash = true
+
+[settings]
+file_path = "/Users/martinnorgaard/Documents/GitHub/mriqc/mriqc/data/pet/derivatives/mriqc/logs/config-20250509-150839_62d91c5f-fc2a-4ed5-87b2-8c474d5e033e.toml"
+start_time = 1746796119.322388
+
+[execution.bids_filters]
+
+[workflow.biggest_file_gb]
+pet = 0.04553897213190794
+
+[nipype.plugin_args]
+maxtasksperchild = 1
+raise_insufficient = false
+n_procs = 10
diff --git a/mriqc/data/pet/derivatives/petprep_hmc/dataset_description.json b/mriqc/data/pet/derivatives/petprep_hmc/dataset_description.json
@@ -0,0 +1,11 @@
+{
+    "Name": "PETPrep HMC workflow",
+    "DatasetType": "derivative",
+    "BIDSVersion": "1.7.0",
+    "GeneratedBy": [
+        {
+            "Name": "petprep_hmc",
+            "Version": "0.0.10"
+        }
+    ]
+}
diff --git a/...vatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-confounds_timeseries.tsv b/...vatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-confounds_timeseries.tsv
@@ -0,0 +1,22 @@
+	trans_x	trans_y	trans_z	rot_x	rot_y	rot_z	max_x	max_y	max_z	max_tot	median_tot
+0	0.042524	0.033254	0.201559	0.005093	0.002339	0.001308	0.13510399999999834	0.39417200000000463	0.31259900000000584	0.4144521632577178	0.24044795261758672
+1	0.042524	0.033254	0.201559	0.005093	0.002339	0.001308	0.13510399999999834	0.39417200000000463	0.31259900000000584	0.4144521632577178	0.24044795261758672
+2	0.042524	0.033254	0.201559	0.005093	0.002339	0.001308	0.13510399999999834	0.39417200000000463	0.31259900000000584	0.4144521632577178	0.24044795261758672
+3	0.042524	0.033254	0.201559	0.005093	0.002339	0.001308	0.13510399999999834	0.39417200000000463	0.31259900000000584	0.4144521632577178	0.24044795261758672
+4	0.062664	0.167271	-0.256301	0.00418	0.003669	0.002652	0.2502160000000089	0.388264999999997	0.5241060000000033	0.6028335918327759	0.3463396698610647
+5	0.168891	0.343776	-0.780523	0.000624	0.003962	0.001453	0.2699439999999953	0.3434820000000016	0.7194990000000061	0.799197440563345	0.63273720463041
+6	0.106591	0.272566	-0.564354	0.000642	0.002471	0.000904	0.1644629999999978	0.2901329999999973	0.5417169999999984	0.6110877928898555	0.5080529114299173
+7	0.13754	0.27817	-0.548284	0.001489	0.003523	0.00127	0.21731200000000683	0.34546000000000276	0.5598179999999999	0.6425998955306523	0.4926435889280838
+8	0.174567	0.222818	-0.554918	0.001433	0.003675	0.001076	0.23878399999999544	0.2927350000000004	0.5558189999999996	0.618726189759256	0.465822407279853
+9	0.147141	0.287726	-0.520696	0.000968	0.00332	0.001259	0.21775800000000345	0.31749599999999845	0.4967269999999999	0.5849997671324294	0.44919262281229305
+10	0.135763	0.294311	-0.862506	-0.002533	0.003885	0.001593	0.23634099999999592	0.20630599999999788	0.6611520000000013	0.6748301069350773	0.4783911898636546
+11	0.133987	0.316514	-0.895106	-0.004445	0.003294	0.001094	0.20574100000000328	0.2536970000000025	0.6721299999999957	0.6796346486296888	0.4418570389321888
+12	0.128307	0.301193	-0.836072	-0.004811	0.003721	0.001356	0.21856700000000728	0.22622900000000357	0.5877809999999997	0.5904814613203331	0.3421570358811808
+13	0.092678	0.187613	-0.553462	-0.003839	0.003561	0.00176	0.21528600000000608	0.2772340000000071	0.3308460000000011	0.3442636194894741	0.1966820596826297
+14	-0.041942	0.116471	-0.263375	-0.003876	0.00214	0.001622	0.15661199999999553	0.3395190000000028	0.3210550000000012	0.4017416189953524	0.23365494368620213
+15	0.004062	-0.070845	-0.16049	-0.004344	0.001881	0.00033	0.14010300000000342	0.46297400000000266	0.45114199999999727	0.5742322447163773	0.389676632863509
+16	0.007914	-0.104361	-0.187322	-0.005488	0.001501	-4.3e-05	0.1222270000000023	0.5696659999999909	0.5147029999999972	0.6719007325111281	0.4528683969156977
+17	-0.076009	-0.128338	0.00757	-0.005087	0.001424	0.000657	0.16710299999999734	0.6089350000000024	0.6598400000000026	0.8121806209144716	0.5925741595733051
+18	-0.073613	-0.212594	0.01942	-0.004817	0.001732	0.000646	0.19015100000000018	0.6689420000000084	0.667942999999994	0.8669613148820281	0.6566910918807108
+19	-0.019034	-0.430565	0.448751	-0.002102	0.001828	-0.000195	0.1856509999999929	0.5980779999999939	0.8220900000000029	0.9870592088841462	0.8726034584787558
+20	-0.016395	-0.801118	0.663921	-0.004665	-0.003338	-0.003624	0.28188299999999344	1.0198799999999935	0.9927750000000017	1.3441046995145112	1.0747232794021842
diff --git a/...data/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-mc_pet.json b/...data/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-mc_pet.json
@@ -0,0 +1,13 @@
+{
+    "Description": "Motion-corrected PET file",
+    "Sources": "/Users/martinnorgaard/Downloads/eddymotion_pet_testdata/data/sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.nii.gz",
+    "ReferenceImage": "Robust template using mri_robust_register",
+    "CostFunction": "ROB",
+    "MCTreshold": "20",
+    "MCFWHM": "10",
+    "MCStartTime": "60",
+    "QC": "",
+    "SoftwareName": "PETPrep HMC workflow",
+    "SoftwareVersion": "0.0.10",
+    "CommandLine": "run.py /Users/martinnorgaard/Downloads/eddymotion_pet_testdata/data/ /Users/martinnorgaard/Downloads/eddymotion_pet_testdata/data/derivatives/petprep_hmc participant --n_procs 6 --mc_start_time 60"
+}
diff --git a/...ta/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-mc_pet.nii.gz b/...ta/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-mc_pet.nii.gz
diff --git a/...rivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-movement.png b/...rivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-movement.png
diff --git a/...rivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-rotation.png b/...rivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-rotation.png
diff --git a/...atives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-translation.png b/...atives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-translation.png
diff --git a/...rep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-with_motion_correction.gif b/...rep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-with_motion_correction.gif
diff --git a/..._hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-without_motion_correction.gif b/..._hmc/sub-01/ses-baseline/sub-01_ses-baseline_desc-without_motion_correction.gif
diff --git a/mriqc/data/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_report.html b/mriqc/data/pet/derivatives/petprep_hmc/sub-01/ses-baseline/sub-01_ses-baseline_report.html
@@ -0,0 +1,6 @@
+<html><head><title>Motion Correction Report</title></head><body><h2>PET with Motion Correction</h2><p>PET scan with motion correction applied. This shows the stabilized sequence.
+</p><img src='sub-01_ses-baseline_desc-with_motion_correction.gif' style='width:100%; max-width:600px'><br><h2>PET without Motion Correction</h2><p>Original PET scan without any motion correction. Notice the movements affecting the quality.
+</p><img src='sub-01_ses-baseline_desc-without_motion_correction.gif' style='width:100%; max-width:600px'><br><h2>Movement Metrics</h2><p>Overall movement metrics over time.
+</p><img src='sub-01_ses-baseline_desc-movement.png' style='width:100%; max-width:600px'><br><h2>Rotation Metrics</h2><p>Rotation components of motion correction.
+</p><img src='sub-01_ses-baseline_desc-rotation.png' style='width:100%; max-width:600px'><br><h2>Translation Metrics</h2><p>Translation components of motion correction.
+</p><img src='sub-01_ses-baseline_desc-translation.png' style='width:100%; max-width:600px'><br></body></html>
diff --git a/mriqc/data/pet/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii b/mriqc/data/pet/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii
diff --git a/mriqc/data/pet/sub-01/ses-baseline/pet/.Rhistory b/mriqc/data/pet/sub-01/ses-baseline/pet/.Rhistory
diff --git a/mriqc/data/pet/sub-01/ses-baseline/pet/.nfs000000073462970e000001f1 b/mriqc/data/pet/sub-01/ses-baseline/pet/.nfs000000073462970e000001f1