[ENH] Bep 009: Positron Emission Tomography

bids-validator/bids_validator/rules/file_level_rules.json

@@ -500,5 +500,25 @@
 
   "stimuli": {
     "regexp": "^[\\/\\\\](?:stimuli)[\\/\\\\](?:.*)$"
+  },
+
+  "pet": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?pet[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_task-[a-zA-Z0-9]+)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?_(@@@_pet_ext_@@@)$",
+    "tokens": {
+      "@@@_pet_ext_@@@": [
+        "pet\\.nii\\.gz",
+        "pet\\.nii",
+        "pet\\.json",
+        "events\\.json",
+        "events\\.tsv"
+      ]
+    }
+  },
+
+  "pet_blood": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?pet[\\/\\\\](sub-[a-zA-Z0-9]+)(?:(_ses-[a-zA-Z0-9]+))?(?:_task-[a-zA-Z0-9]+)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_recording-[a-zA-Z0-9]+)?_(@@@_pet_ext_@@@)$",
+    "tokens": {
+      "@@@_pet_ext_@@@": ["blood\\.tsv\\.gz", "blood\\.tsv", "blood\\.json"]
+    }
   }
 }

bids-validator/bids_validator/rules/session_level_rules.json

@@ -32,6 +32,17 @@
     }
   },
 
+  "pet_ses": {
+    "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_trc-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_task-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_pet_ses_type_@@@)$",
+    "tokens": {
+      "@@@_pet_ses_type_@@@": [
+        "_pet.json",
+        "_events.json",
+        "_events.tsv"
+      ]
+    }
+  },
+
   "anat_ses": {
     "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?\\1(_\\2)?(?:_acq-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+_)?(@@@_anat_ses_type_@@@).json$",
     "tokens": {

bids-validator/bids_validator/rules/top_level_rules.json

@@ -46,6 +46,15 @@
     }
   },
 
+  "pet_top": {
+    "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:trc-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:task-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_pet_suffixes_@@@)\\.json$",
+    "tokens": {
+      "@@@_pet_suffixes_@@@": [
+        "pet"
+      ]
+    }
+  },
+
   "anat_top": {
     "regexp": "^[\\/\\\\](?:ses-[a-zA-Z0-9]+_)?(?:acq-[a-zA-Z0-9]+_)?(?:rec-[a-zA-Z0-9]+_)?(?:run-[0-9]+_)?(@@@_anat_suffixes_@@@)\\.json$",
     "tokens": {

bids-validator/bids_validator/tsv/non_custom_columns.json

@@ -43,5 +43,6 @@
   "phenotype": ["participant_id"],
   "scans": ["acq_time", "filename"],
   "sessions": ["acq_time", "session_id"],
-  "aslcontext": ["volume_type"]
+  "aslcontext": ["volume_type"],
+  "blood": ["time", "plasma_radioactivity", "whole_blood_radioactivity", "metabolite_parent_fraction", "hplc_recovery_fractions"]
 }

bids-validator/tests/bids.spec.js

@@ -273,12 +273,35 @@ describe('BIDS example datasets ', function() {
       isdone()
     })
   })
-  it('should throw an error if it encounters a non-utf-8 file', function(isdone) {
+
+  it('should validate pet data', function(isdone) {
+    validate.BIDS(
+      createDatasetFileList('broken_pet_example_2-pet_mri'),
+      options,
+      function(issues) {
+        assertErrorCode(issues.errors, 55)
+        isdone()
+      },
+    )
+  })
+
+  it('should validate pet blood data', function(isdone) {
+    validate.BIDS(
+      createDatasetFileList('broken_pet_example_3-pet_blood'),
+      options,
+      function(issues) {
+        assertErrorCode(issues.errors, 55)
+        isdone()
+      },
+    )
+  })
+
+  it('should catch missing tsv columns', function(isdone) {
     validate.BIDS(
-      createDatasetFileList('latin-1_description'),
+      createDatasetFileList('pet_blood_missing_tsv_column'),
       options,
       function(issues) {
-        assertErrorCode(issues.errors, 123)
+        assertErrorCode(issues.errors, 211)
         isdone()
       },
     )

bids-validator/tests/data/broken_pet_example_2-pet_mri/README

@@ -0,0 +1,6 @@
+This dataset consists of a single PET measurement of a human brain using [11C]DASB to measure serotonin transporter availability. An anatomical T1-weighted MRI is also available. There are no arterial measurements available for this tracer.
+
+It has been broken for testing purposes. Changes made (in /sub-01/ses-01/pet/sub-01_ses-01_pet.json):
+- Manufacturer set to a number (expecting string).
+- InjectedMass removed (required).
+- TracerMolecularWeightUnit removed (required when TracerMolecularWeight is set).

bids-validator/tests/data/broken_pet_example_2-pet_mri/dataset_description.json

@@ -0,0 +1,17 @@
+{
+  "BIDSVersion": "1.0.2",
+  "License": "CCO license",
+  "Name": "[11C]DASB PET Cimbi database example",
+  "Authors": [
+    "Melanie Ganz-Benjaminsen",
+    "Martin Noergaard"
+  ],
+  "Acknowledgements": "Knudsen GM, Jensen PS, Erritzoe D, Baaré WFC, Ettrup A, Fisher PM, Gillings N, Hansen HD, Hansen LK, Hasselbalch SG, Henningsson S, Herth MM, Holst KK, Iversen P, Kessing LV, Macoveanu J, Madsen KS, Mortensen EL, Nielsen FÅ, Paulson OB, Siebner HR, Stenbæk DS, Svarer C, Jernigan TL, Strother SC, Frokjaer VG. The Center for Integrated Molecular Brain Imaging (Cimbi) Database. NeuroImage. 2016 Jan 1;124(Pt B):1213-1219",
+  "HowToAcknowledge": "This data was obtained from the Cimbi database.",
+  "Funding": [
+    "Lundbeck Foundation R90-A7722",
+    "Danish Research Council 09-063598",
+    "Rigshospitalet"
+  ],
+  "DatasetDOI": ""
+}

bids-validator/tests/data/broken_pet_example_2-pet_mri/participants.json

@@ -0,0 +1,18 @@
+{
+  "participant_id":{
+    "LongName":"Participant Id",
+    "Description":"label identifying a particular subject"
+  },
+  "weight":{
+    "LongName":"Weight",
+    "Description":"Weight of the participant",
+    "Units": "kg"
+  },
+  "sex":{
+    "LongName":"Sex",
+    "Description":"Sex of the participant",
+    "Levels": {
+      "M": "male", "F": "female"
+    }
+  }
+}

bids-validator/tests/data/broken_pet_example_2-pet_mri/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	weight	sex
+sub-01	50	F

bids-validator/tests/data/broken_pet_example_2-pet_mri/sub-01/ses-01/anat/sub-01_ses-01_T1w.json

@@ -0,0 +1,37 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Trio",
+	"InstitutionName": "DRCMR_HVIDOVRE",
+	"InstitutionAddress": "30Kettegaard_Alle_Copenhagen_Hvidovre_DK-2650_DK",
+	"DeviceSerialNumber": "20511",
+	"StationName": "MRC20511",
+	"ProcedureStepDescription": "Hjerne_projekter_Cimbi_SAD",
+	"SoftwareVersions": "syngo_MR_A30_4VA30A",
+	"SeriesDescription": "t1_mpr_ns_sag_1mm_noring",
+	"ProtocolName": "t1_mpr_ns_sag_1mm_noring",
+	"ScanningSequence": "IR_GR",
+	"SequenceVariant": "SP_MP",
+	"ScanOptions": "IR",
+	"SequenceName": "_tfl3d1_ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"],
+	"AcquisitionTime": "10:24:59.860010",
+	"AcquisitionNumber": 1,
+	"ImageComments": "50524",
+	"EchoTime": 0.00304,
+	"RepetitionTime": 1.55,
+	"InversionTime": 0.8,
+	"FlipAngle": 9,
+	"PartialFourier": 1,
+	"BaseResolution": 256,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "8_Channel_Head",
+	"PulseSequenceDetails": "%SiemensSeq%_tfl",
+	"PercentPhaseFOV": 100,
+	"PhaseEncodingSteps": 256,
+	"AcquisitionMatrixPE": 256,
+	"ReconMatrixPE": 256,
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20170923 (OpenJPEG build) GCC4.8.4"
+}

bids-validator/tests/data/broken_pet_example_2-pet_mri/sub-01/ses-01/pet/sub-01_ses-01_pet.json

@@ -0,0 +1,39 @@
+{
+        "Modality": "PET",
+        "Manufacturer": 1234,
+        "ManufacturersModelName": "High-Resolution Research Tomograph (HRRT, CTI/Siemens)",
+        "BodyPart": "Brain",
+        "Units": "Bq/ml",
+        "TracerName": "DASB",
+        "TracerRadionuclide": "C11",
+        "TracerMolecularWeight": 282.39,
+        "InjectedRadioactivity": 598,
+        "InjectedRadioactivityUnits": "MBq",
+        "InjectedMassUnits": "ug",
+        "SpecificRadioactivity": 842.25,
+        "SpecificRadioactivityUnits": "MBq/ug",
+        "MolarActivity": 238.23,
+        "MolarActivityUnits": "GBq/umol",
+        "TimeZero": "13:06:34",
+        "ScanStart": 0,
+        "InjectionStart": 0,
+        "ModeOfAdministration": "bolus",
+        "FrameTimesStart": [0, 10, 20, 30, 40, 50, 60, 80, 100, 120, 150, 180, 210, 240, 270, 300, 360, 420, 480, 540, 600, 720, 840, 960, 1080, 1200, 1500, 1800, 2100, 4521, 4800, 5100],
+        "FrameDuration": [10, 20, 30, 40, 50, 60, 80, 100, 120, 150, 180, 210, 240, 270, 300, 360, 420, 480, 540, 600, 720, 840, 960, 1080, 1200, 1500, 1800, 2100, 2337, 4800, 5100, 5400],
+        "AcquisitionMode": "list mode",
+        "ImageDecayCorrected": true,
+        "ImageDecayCorrectionTime": 0,
+        "ReconMatrixSize": [256,256,207,36],
+        "ImageVoxelSize": [1.2188,1.2188,1.2188],
+        "ReconMethodName": "3D-OSEM-PSF",
+        "ReconMethodParameterLabels": ["subsets","iterations"],
+        "ReconMethodParameterUnits": ["none","none"],
+        "ReconMethodParameterValues": [16,10],
+        "ReconFilterType": "none",
+        "ReconFilterSize": 0,
+        "AttenuationCorrection": "[137Cs]transmission scan-based",
+        "PlasmaAvail": false,
+        "MetaboliteAvail": false,
+        "ContinuousBloodAvail": false,
+        "DiscreteBloodAvail": false
+}

bids-validator/tests/data/broken_pet_example_3-pet_blood/README

@@ -0,0 +1,3 @@
+This dataset consists of a single PET measurement of a human brain using [11C]DASB to measure serotonin transporter availability. An anatomical T1-weighted MRI is also available. There are arterial measurements available for this tracer. Note: all image files are empty for privacy reasons. 
+
+IMPORTANT: The molar activity is fixed for all subjects (55 MBq/nmol) given Parsey et al. 2007. 

bids-validator/tests/data/broken_pet_example_3-pet_blood/dataset_description.json

@@ -0,0 +1,7 @@
+{"BIDSVersion":"1.0.4",
+    "License":"CCO license",
+    "Name":"[11C]DASB data set",
+    "Authors":["Martin Norgaard","Christine Delorenzo","Ramin Parsey"],
+    "Acknowledgements":"We thank the employees of the Brain Imaging Core of the NIMH-funded Conte Translational Neuroscience Center, the Kreitchman PET Center, and the Columbia University Radioligand Laboratory for expert help. This work was supported in part by an investigator-initiated grant from Pfizer Inc.",
+    "HowToAcknowledge":"Ramin Parsey, Christine Delorenzo",
+    "DatasetDOI":""}

bids-validator/tests/data/broken_pet_example_3-pet_blood/participants.json

@@ -0,0 +1,9 @@
+{
+  "participant_id":{
+    "LongName":"Participant Id",
+    "Description":"label identifying a particular subject"
+  },
+  "sex":{
+    "LongName":"Sex"
+  }
+}

bids-validator/tests/data/broken_pet_example_3-pet_blood/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex
+sub-01	F

bids-validator/tests/data/broken_pet_example_3-pet_blood/sub-01/ses-01/pet/sub-01_ses-01_pet.json

@@ -0,0 +1,43 @@
+{       
+        "Manufacturer": "Siemens",
+        "ManufacturersModelName": "Siemens HR+",
+        "BodyPart": "Brain",
+        "Units": "Bq/mL",
+        "TracerName": "DASB",
+        "TracerRadionuclide": "C11",
+        "TracerMolecularWeight": 282.39,
+        "TracerMolecularWeightUnits": "g/mol",
+        "TracerInjectionType": "bolus",
+        "InjectedRadioactivity": 694.86,
+        "InjectedRadioactivityUnits": "MBq",
+        "InjectedMass": 3.57,
+        "InjectedMassUnits": "ug",
+        "SpecificRadioactivity": 194.64,
+        "SpecificRadioactivityUnits": "MBq/ug",
+        "MolarActivity": 55,
+        "MolarActivityUnits": "MBq/nmol",
+        "ModeOfAdministration": "bolus",
+        "ScanStart": 0,
+        "InjectionStart": 0,
+        "InjectionEnd": 30,
+        "TimeZero": "12:24:37",
+        "FrameTimesStart": [0, 20, 40, 60, 120, 180, 240, 360, 480, 600, 900, 1200, 1800, 2400, 3000, 3600, 4200, 4800, 5400, 6000, 6600],
+        "FrameDuration": [20, 40, 60, 120, 180, 240, 360, 480, 600, 900, 1200, 1800, 2400, 3000, 3600, 4200, 4800, 5400, 6000, 6600, 7200],
+        "AcquisitionMode": "list mode",
+        "ImageDecayCorrected": true,
+        "ImageDecayCorrectionTime": 0,
+        "ReconMethodName": "Vendor",
+        "ReconMethodParameterLabels": ["Zoom factor"],
+        "ReconMethodParameterUnits": ["none"],
+        "ReconMethodParameterValues": [4],
+        "ReconFilterType": ["Image filter were Shepp 0.5","the Z filter was all-pass 0.4"],
+        "ReconFilterSize": [2.5, 2.0],
+        "AttenuationCorrection": "Transmission data, and scatter was corrected using a model-based method",
+        "AttenuationCorrectionMethodReference": "Parsey et al. 2006, Metabolite considerations in the in vivo quantification of serotonin transporters using 11C-DASB and PET in humans, Journal of Nuclear Medicine",
+        "PlasmaAvail": true,
+        "MetaboliteAvail": true,
+        "ContinuousBloodAvail": false,
+        "DiscreteBloodAvail": false,
+        "MetaboliteMethod": "Bioscan g-detector",
+        "MetaboliteRecoveryCorrectionApplied": false
+}

bids-validator/tests/data/broken_pet_example_3-pet_blood/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.json

@@ -0,0 +1,21 @@
+{
+  "PlasmaAvail": true,
+
+  "MetaboliteAvail": true,
+  "MetaboliteMethod": "Bioscan g-detector",
+  "MetaboliteRecoveryCorrectionApplied": false,
+  "DispersionCorrected": false,
+
+  "time": {
+    "Description": "Time in relation to time zero defined by the _pet.json",
+    "Units": "s"
+  },
+  "plasma_radioactivity": {
+    "Description": "Radioactivity in plasma samples",
+    "Units": "Bq/ml"
+  },
+  "metabolite_parent_fraction": {
+    "Description": "Parent fraction of the radiotracer. The metabolite and unmetabolized parent compound were collected in separate vials, and radioactivity was quantified using a Bioscan g-detector after correction for background radioactivity.",
+    "Units": "unitless"
+  }
+}

bids-validator/tests/data/broken_pet_example_3-pet_blood/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.tsv

@@ -0,0 +1,33 @@
+time	plasma_radioactivity	metabolite_parent_fraction
+0	0	n/a
+10.0000002	22.62883	n/a
+19.9999998	57.2612	n/a
+30	1836.01696	n/a
+40.002	14344.6921	n/a
+49.998	23636.8654	n/a
+60	31688.6211	n/a
+70.002	33226.4655	n/a
+79.998	26847.9352	n/a
+90	20327.9066	n/a
+100.002	17169.8248	n/a
+109.998	15198.5614	n/a
+120	14509.6888	0.50774032
+139.998	13080.8694	n/a
+160.002	11937.2848	n/a
+180	11422.8402	n/a
+199.998	10905.5509	n/a
+220.002	10870.4076	n/a
+240	16745.3205	n/a
+360	8193.32255	n/a
+480	9180.87697	n/a
+720	8957.52869	0.55283186
+960	8500.14505	n/a
+1200	8846.04732	0.35144152
+1800	8805.56451	n/a
+2400	8707.26365	n/a
+3000	9078.7899	0.1507185
+3600	8356.09036	n/a
+4800	8095.22519	0.10388412
+5400	7480.43763	n/a
+6000	7099.9559	0.09530672
+7200	6279.54565	n/a

bids-validator/tests/data/pet_blood_missing_tsv_column/README

@@ -0,0 +1,3 @@
+This dataset consists of a single PET measurement of a human brain using [11C]DASB to measure serotonin transporter availability. An anatomical T1-weighted MRI is also available. There are arterial measurements available for this tracer. Note: all image files are empty for privacy reasons. 
+
+IMPORTANT: The molar activity is fixed for all subjects (55 MBq/nmol) given Parsey et al. 2007. 

bids-validator/tests/data/pet_blood_missing_tsv_column/dataset_description.json

@@ -0,0 +1,7 @@
+{"BIDSVersion":"1.0.4",
+    "License":"CCO license",
+    "Name":"[11C]DASB data set",
+    "Authors":["Martin Norgaard","Christine Delorenzo","Ramin Parsey"],
+    "Acknowledgements":"We thank the employees of the Brain Imaging Core of the NIMH-funded Conte Translational Neuroscience Center, the Kreitchman PET Center, and the Columbia University Radioligand Laboratory for expert help. This work was supported in part by an investigator-initiated grant from Pfizer Inc.",
+    "HowToAcknowledge":"Ramin Parsey, Christine Delorenzo",
+    "DatasetDOI":""}

bids-validator/tests/data/pet_blood_missing_tsv_column/participants.json

@@ -0,0 +1,9 @@
+{
+  "participant_id":{
+    "LongName":"Participant Id",
+    "Description":"label identifying a particular subject"
+  },
+  "sex":{
+    "LongName":"Sex"
+  }
+}

bids-validator/tests/data/pet_blood_missing_tsv_column/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex
+sub-01	F