[FIX] PET Spec; added known DICOM tags, fixed tag error, updated cita…

…tion, clarified scale factor. (#1021) * PET citation update * DICOM tag error fix * scale factor should be 1 (does it work as 'array') * added all DICOM tags we know * Update 09-positron-emission-tomography.md Added dicom tag description for `InjectionStart` * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Update src/04-modality-specific-files/09-positron-emission-tomography.md Co-authored-by: Taylor Salo <[email protected]> * Fixed markdown formatting, removed dicom tag desc - Fixed markdown formatting in src/01-introduction.md - Removed dicom tag description for InjectionTimeStart in src/04-modality-specific-files/09-positron-emission-tomography.md as there is some disagreement on whether dicom tag Radiopharmaceutical Start Time (0018, 1072) should be referenced. * added back tag to description, dropped reference to timezero * Update metadata.yaml Update Scale Factor description to consensus * removed trailing spaces. * update text "recommended" to "RECOMMENDED" Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: CPernet <[email protected]> Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Martin Norgaard <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]>
bids-standard · Mar 31, 2022 · 4428fd3 · 4428fd3
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diff --git a/src/01-introduction.md b/src/01-introduction.md
@@ -113,12 +113,22 @@ For example:
 
 #### PET
 
+-   Norgaard, M., Matheson, G.J., Hansen, H.D., Thomas, A., Searle, G., Rizzo, G.,
+    Veronese, M., Giacomel, A., Yaqub, M., Tonietto, M., Funck, T., Gillman, A., Boniface,
+    H., Routier, A., Dalenberg, J.R.., Betthauser, T., Feingold, F., Markiewicz, C.J.,
+    Gorgolewski, K.J., Blair, R.W., Appelhoff, S., Gau, R., Salo, T., Niso, G., Pernet, C.,
+    Phillips, C., Oostenveld, R., Gallezot, J-D., Carson, R.E., Knudsen, G.M.,
+    Innis R.B. & Ganz M. (2021).
+    **PET-BIDS, an extension to the brain imaging data structure for positron emission tomography**.
+    Scientific Data, 9 (65).
+    [doi:10.1038/s41597-022-01164-1](https://doi.org/10.1038/s41597-022-01164-1)
+
 -   Knudsen GM, Ganz M, Appelhoff S, Boellaard R, Bormans G, Carson RE, Catana C,
     Doudet D, Gee AD, Greve DN, Gunn RN, Halldin C, Herscovitch P, Huang H, Keller SH,
     Lammertsma AA, Lanzenberger R, Liow JS, Lohith TG, Lubberink M, Lyoo CH, Mann JJ,
     Matheson GJ, Nichols TE, Nørgaard M, Ogden T, Parsey R, Pike VW, Price J, Rizzo G,
-    Rosa-Neto P, Schain M, Scott PJH, Searle G, Slifstein M, Suhara T, Talbot PS,
-    Thomas A, Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. (2020).
+    Rosa-Neto P, Schain M, Scott PJH, Searle G, Slifstein M, Suhara T, Talbot PS, Thomas A,
+    Veronese M, Wong DF, Yaqub M, Zanderigo F, Zoghbi S, Innis RB. (2020).
     **Guidelines for Content and Format of PET Brain Data in Publications and in Archives: A Consensus Paper**.
     Journal of Cerebral Blood Flow and Metabolism, 2020 Aug; 40(8): 1576-1585.
     [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433)

diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -154,8 +154,8 @@ which we divide into several categories:
 
 {{ MACROS___make_metadata_table(
    {
-      "TracerName": "REQUIRED",
-      "TracerRadionuclide": "REQUIRED",
+      "TracerName": ("REQUIRED", "Corresponds to DICOM Tags (0008,0105) `Mapping Resource` and (0008,0122) `Mapping Resource Name`."),
+      "TracerRadionuclide": ("REQUIRED", "Corresponds to DICOM Tags (0008,0104) `CodeValue` and (0008,0104) `CodeMeaning`."),
       "InjectedRadioactivity": "REQUIRED",
       "InjectedRadioactivityUnits": "REQUIRED",
       "InjectedMass": "REQUIRED",
@@ -186,11 +186,11 @@ which we divide into several categories:
 
 {{ MACROS___make_metadata_table(
    {
-      "PharmaceuticalName": "RECOMMENDED",
-      "PharmaceuticalDoseAmount": "RECOMMENDED",
+      "PharmaceuticalName": ("RECOMMENDED", "Corresponds to DICOM Tag (0008,0034) `Intervention Drug Name`."),
+      "PharmaceuticalDoseAmount": ("RECOMMENDED", "Corresponds to DICOM Tag (0008,0028) `Intervention Drug Dose`."),
       "PharmaceuticalDoseUnits": "RECOMMENDED",
       "PharmaceuticalDoseRegimen": "RECOMMENDED",
-      "PharmaceuticalDoseTime": "RECOMMENDED",
+      "PharmaceuticalDoseTime": ("RECOMMENDED", "Corresponds to a combination of DICOM Tags (0008,0027) `Intervention Drug Stop Time` and (0008,0035) `Intervention Drug Start Time`."),
       "Anaesthesia": "OPTIONAL",
    }
 ) }}
@@ -201,11 +201,11 @@ which we divide into several categories:
    {
       "TimeZero": "REQUIRED",
       "ScanStart": "REQUIRED",
-      "InjectionStart": "REQUIRED",
+      "InjectionStart": ("REQUIRED", "This corresponds to DICOM Tag (0018,1072) `Radiopharmaceutical Start Time`."),
       "FrameTimesStart": "REQUIRED",
       "FrameDuration": "REQUIRED",
-      "InjectionEnd": "RECOMMENDED",
-      "ScanDate": "DEPRECATED",
+      "InjectionEnd": ("RECOMMENDED", "This corresponds to DICOM Tag (0018,1073) `Radiopharmaceutical Stop Time` converted to seconds relative to TimeZero."),
+      "ScanDate": ("DEPRECATED", "This corresponds to DICOM Tag (0008,0022) `Acquisition Date`."),
    }
 ) }}
 
@@ -218,19 +218,19 @@ We refer to the common principles for the standards for describing dates and tim
       "AcquisitionMode": "REQUIRED",
       "ImageDecayCorrected": "REQUIRED",
       "ImageDecayCorrectionTime": "REQUIRED",
-      "ReconMethodName": "REQUIRED",
-      "ReconMethodParameterLabels": "REQUIRED",
-      "ReconMethodParameterUnits": "REQUIRED",
-      "ReconMethodParameterValues": "REQUIRED",
-      "ReconFilterType": "REQUIRED",
-      "ReconFilterSize": "REQUIRED",
-      "AttenuationCorrection": "REQUIRED",
+      "ReconMethodName": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterLabels": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterUnits": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconMethodParameterValues": ("REQUIRED", "This partly matches the DICOM Tag (0054,1103) `Reconstruction Method`."),
+      "ReconFilterType": ("REQUIRED", "This partly matches the DICOM Tag (0018,1210) `Convolution Kernel`."),
+      "ReconFilterSize": ("REQUIRED", "This partly matches the DICOM Tag (0018,1210) `Convolution Kernel`."),
+      "AttenuationCorrection": ("REQUIRED", "This corresponds to DICOM Tag (0054,1101) `Attenuation Correction Method`."),
       "ReconMethodImplementationVersion": "RECOMMENDED",
       "AttenuationCorrectionMethodReference": "RECOMMENDED",
       "ScaleFactor": "RECOMMENDED",
-      "ScatterFraction": "RECOMMENDED",
-      "DecayCorrectionFactor": "RECOMMENDED",
-      "DoseCalibrationFactor": "RECOMMENDED",
+      "ScatterFraction": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1323) `Scatter Fraction Factor`."),
+      "DecayCorrectionFactor": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1321) `Decay Factor`."),
+      "DoseCalibrationFactor": ("RECOMMENDED", "This corresponds to DICOM Tag (0054,1322) `Dose Calibration Factor`."),
       "PromptRate": "RECOMMENDED",
       "RandomRate": "RECOMMENDED",
       "SinglesRate": "RECOMMENDED",

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
@@ -1247,7 +1247,7 @@ InjectionStart:
   description: |
     Time of start of injection with respect to `"TimeZero"` in the default unit
     seconds.
-    This corresponds to DICOM Tag 0018, 1042 `Contrast/Bolus Start Time`
+    This corresponds to DICOM Tag 0018, 1072 `Contrast/Bolus Start Time`
     converted to seconds relative to `"TimeZero"`.
   type: number
   unit: s
@@ -2293,7 +2293,9 @@ SamplingFrequency:
 ScaleFactor:
   name: ScaleFactor
   description: |
-    Scale factor for each frame.
+    Scale factor for each frame. This field MUST be defined if the imaging data (`.nii[.gz]`) are scaled.
+    If this field is not defined, then it is assumed that the scaling factor is 1. Defining this field
+    when the scaling factor is 1 is RECOMMENDED, for the sake of clarity.
   type: array
   items:
     type: number