From 1ddcd31bc4c2832125e159a8521354241731ddb8 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:00:33 -0500 Subject: [PATCH 1/6] add example for ReconFilterType is 'none' --- pet006/README | 2 ++ pet006/dataset_description.json | 7 ++++++ pet006/participants.json | 9 +++++++ pet006/participants.tsv | 2 ++ pet006/sub-01/pet/sub-01_pet.json | 38 +++++++++++++++++++++++++++++ pet006/sub-01/pet/sub-01_pet.nii.gz | 1 + 6 files changed, 59 insertions(+) create mode 100644 pet006/README create mode 100644 pet006/dataset_description.json create mode 100644 pet006/participants.json create mode 100644 pet006/participants.tsv create mode 100755 pet006/sub-01/pet/sub-01_pet.json create mode 100755 pet006/sub-01/pet/sub-01_pet.nii.gz diff --git a/pet006/README b/pet006/README new file mode 100644 index 000000000..94d907bce --- /dev/null +++ b/pet006/README @@ -0,0 +1,2 @@ +This dataset consists of a single calibration scan done on a Phantom, it's primary use is to ensure the behavior defined by the BIDS Speficication wrt to +If ReconMethodParameters = ['none']; then ReconFilterSize is optional and ReconMethodParameterLabels = ['none'] are valid. diff --git a/pet006/dataset_description.json b/pet006/dataset_description.json new file mode 100644 index 000000000..cac4b2e6e --- /dev/null +++ b/pet006/dataset_description.json @@ -0,0 +1,7 @@ +{"BIDSVersion":"1.9.0", + "License":"CCO license", + "Name":"BIDS Example Dataset PET 006", + "Authors":["Murat Bilgel", "Cyril Pernet", "Anthony Galassi"], + "Acknowledgements":"John Hopkins University PET team for scanning this phantom.", + "Funding":["Not Sure"], + "DatasetDOI":""} \ No newline at end of file diff --git a/pet006/participants.json b/pet006/participants.json new file mode 100644 index 000000000..6808255ce --- /dev/null +++ b/pet006/participants.json @@ -0,0 +1,9 @@ +{ + "participant_id":{ + "LongName":"Participant Id", + "Description":"label identifying a particular subject" + }, + "weight":{ + "LongName":"Weight" + } +} \ No newline at end of file diff --git a/pet006/participants.tsv b/pet006/participants.tsv new file mode 100644 index 000000000..672318828 --- /dev/null +++ b/pet006/participants.tsv @@ -0,0 +1,2 @@ +participant_id weight +sub-01 4 diff --git a/pet006/sub-01/pet/sub-01_pet.json b/pet006/sub-01/pet/sub-01_pet.json new file mode 100755 index 000000000..6fe04fb68 --- /dev/null +++ b/pet006/sub-01/pet/sub-01_pet.json @@ -0,0 +1,38 @@ +{ + "AcquisitionMode": "list mode", + "AttenuationCorrection": "measured(emission present), 0.096000 cm-1, attenuation smooth", + "AttenuationCorrectionMethod": "measured(emission present), 0.096000 cm-1, attenuation smooth", + "BodyPart": "Phantom", + "DecayCorrectionFactor": [1.42614], + "DoseCalibrationFactor": 1323, + "FrameDuration": [98000], + "FrameTimesStart": [0], + "ImageDecayCorrected": true, + "ImageDecayCorrectionTime": 0, + "InjectedMass": 181149988.3691438, + "InjectedMassUnits": "ug", + "InjectedRadioactivity": 75.84999999999999, + "InjectedRadioactivityUnits": "MBq", + "InjectedVolume": 0, + "InjectionStart": 0, + "InstitutionName": "NIH Clinical Center, USA", + "Manufacturer": "GE MEDICAL SYSTEMS", + "ManufacturersModelName": "GE Advance", + "ModeOfAdministration": "infusion", + "ReconFilterSize": [0], + "ReconFilterType": "None", + "ReconMethodName": "3D Kinahan - Rogers", + "ReconMethodParameterLabels": [ + "none" + ], + "ReconParameterUnits": "none", + "ScanStart": 0, + "ScatterCorrectionMethod": "Gaussian Fit", + "SpecificRadioactivity": 418713.8, + "SpecificRadioactivityUnits": "Bq/g", + "TimeZero": "12:44:31", + "TracerName": "FDG", + "TracerRadionuclide": "F18", + "Units": "Bq/mL", + "filename": "D:\\BIDS\\ONP\\OpenNeuroPET-Phantoms\\sub-GeneralElectricAdvanceJHU\\pet\\sub-GeneralElectricAdvanceJHU_pet.json" + } \ No newline at end of file diff --git a/pet006/sub-01/pet/sub-01_pet.nii.gz b/pet006/sub-01/pet/sub-01_pet.nii.gz new file mode 100755 index 000000000..8b1378917 --- /dev/null +++ b/pet006/sub-01/pet/sub-01_pet.nii.gz @@ -0,0 +1 @@ + From ac4061ed56a44193fe1bd37895ed27f679056fd6 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:12:02 -0500 Subject: [PATCH 2/6] Apply suggestions from code review whoops --- pet006/sub-01/pet/sub-01_pet.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/pet006/sub-01/pet/sub-01_pet.json b/pet006/sub-01/pet/sub-01_pet.json index 6fe04fb68..48f7e6b55 100755 --- a/pet006/sub-01/pet/sub-01_pet.json +++ b/pet006/sub-01/pet/sub-01_pet.json @@ -19,13 +19,11 @@ "Manufacturer": "GE MEDICAL SYSTEMS", "ManufacturersModelName": "GE Advance", "ModeOfAdministration": "infusion", - "ReconFilterSize": [0], "ReconFilterType": "None", "ReconMethodName": "3D Kinahan - Rogers", "ReconMethodParameterLabels": [ "none" ], - "ReconParameterUnits": "none", "ScanStart": 0, "ScatterCorrectionMethod": "Gaussian Fit", "SpecificRadioactivity": 418713.8, From 6833cbeefcf2db325bf5045f7926cf7792bcf0a2 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:12:23 -0500 Subject: [PATCH 3/6] Update sub-01_pet.json add newline --- pet006/sub-01/pet/sub-01_pet.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pet006/sub-01/pet/sub-01_pet.json b/pet006/sub-01/pet/sub-01_pet.json index 48f7e6b55..adf6ea9a0 100755 --- a/pet006/sub-01/pet/sub-01_pet.json +++ b/pet006/sub-01/pet/sub-01_pet.json @@ -33,4 +33,4 @@ "TracerRadionuclide": "F18", "Units": "Bq/mL", "filename": "D:\\BIDS\\ONP\\OpenNeuroPET-Phantoms\\sub-GeneralElectricAdvanceJHU\\pet\\sub-GeneralElectricAdvanceJHU_pet.json" - } \ No newline at end of file + } From 2d41f1f34ddc89e65b046e4aac31a760eb95ebab Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:13:17 -0500 Subject: [PATCH 4/6] Apply suggestions from code review add more newlines --- pet006/dataset_description.json | 2 +- pet006/participants.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pet006/dataset_description.json b/pet006/dataset_description.json index cac4b2e6e..a61f93365 100644 --- a/pet006/dataset_description.json +++ b/pet006/dataset_description.json @@ -4,4 +4,4 @@ "Authors":["Murat Bilgel", "Cyril Pernet", "Anthony Galassi"], "Acknowledgements":"John Hopkins University PET team for scanning this phantom.", "Funding":["Not Sure"], - "DatasetDOI":""} \ No newline at end of file + "DatasetDOI":""} diff --git a/pet006/participants.json b/pet006/participants.json index 6808255ce..d8c8962dc 100644 --- a/pet006/participants.json +++ b/pet006/participants.json @@ -6,4 +6,4 @@ "weight":{ "LongName":"Weight" } -} \ No newline at end of file +} From 7a5b36be9e423f1ae0517df107ae566180196c92 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Mon, 26 Feb 2024 11:32:41 -0500 Subject: [PATCH 5/6] Update pet006/README expanded acronym Co-authored-by: Remi Gau --- pet006/README | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pet006/README b/pet006/README index 94d907bce..9df28221f 100644 --- a/pet006/README +++ b/pet006/README @@ -1,2 +1,2 @@ -This dataset consists of a single calibration scan done on a Phantom, it's primary use is to ensure the behavior defined by the BIDS Speficication wrt to +This dataset consists of a single calibration scan done on a Phantom, it's primary use is to ensure the behavior defined by the BIDS Speficication with respect to If ReconMethodParameters = ['none']; then ReconFilterSize is optional and ReconMethodParameterLabels = ['none'] are valid. From 676a60f5278543234de97721a89150539e546d84 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 29 Feb 2024 16:23:25 -0500 Subject: [PATCH 6/6] Update pet006/sub-01/pet/sub-01_pet.json --- pet006/sub-01/pet/sub-01_pet.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pet006/sub-01/pet/sub-01_pet.json b/pet006/sub-01/pet/sub-01_pet.json index adf6ea9a0..c97905714 100755 --- a/pet006/sub-01/pet/sub-01_pet.json +++ b/pet006/sub-01/pet/sub-01_pet.json @@ -19,7 +19,7 @@ "Manufacturer": "GE MEDICAL SYSTEMS", "ManufacturersModelName": "GE Advance", "ModeOfAdministration": "infusion", - "ReconFilterType": "None", + "ReconFilterType": "none", "ReconMethodName": "3D Kinahan - Rogers", "ReconMethodParameterLabels": [ "none"