Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" #825

Merged
merged 9 commits into from Jul 13, 2021
Merged

[ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" #825

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
139079f
add calibration factor
CPernet Jul 5, 2021
a23ca24
CaibFact --> DoeCalibFact to recon table
CPernet Jul 6, 2021
d031620
fix table cell padding
mnoergaard Jul 6, 2021
41ae130
fix spelling
mnoergaard Jul 6, 2021
436a38a
fix table pipe alignment and description
mnoergaard Jul 6, 2021
2216ec9
better description of DoseCalibrationFactor
CPernet Jul 6, 2021
fbc7a8e
Merge branch 'master' of https://github.com/CPernet/bids-specification
CPernet Jul 6, 2021
0ad9c20
fix table pipe alignment
mnoergaard Jul 6, 2021
7319961
slight change of wording
sappelhoff Jul 6, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
41 changes: 21 additions & 20 deletions src/04-modality-specific-files/09-positron-emission-tomography.md
View file
Open in desktop
Expand Up @@ -196,26 +196,27 @@ We refer to the common principles for the standards for describing dates and tim

#### Reconstruction

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------------------------------ | --------------------- | -------------------------------------- | --------------------------------------------------------------------------------------------------------------- |
| AcquisitionMode | REQUIRED | [string][] | Type of acquisition of the PET data (for example, `"list mode"`) |
| ImageDecayCorrected | REQUIRED | [boolean][] | Boolean flag specifying whether the image data have been decay-corrected. |
| ImageDecayCorrectionTime | REQUIRED | [number][] | Point in time from which the decay correction was applied with respect to TimeZero in the default unit seconds. |
| ReconMethodName | REQUIRED | [string][] | Reconstruction method or algorithm (for example, `"3d-op-osem"`). |
| ReconMethodParameterLabels | REQUIRED | [array][] of [strings][] | Names of reconstruction parameters (for example, `["subsets", "iterations"]`) |
| ReconMethodParameterUnits | REQUIRED | [array][] of [strings][] | Unit of reconstruction parameters (for example, `["none", "none"]`). |
| ReconMethodParameterValues | REQUIRED | [array][] of [numbers][] | Values of reconstruction parameters (for example, `[21, 3]`) |
| ReconFilterType | REQUIRED | [string][] or [array][] of [strings][] | Type of post-recon smoothing (for example, `["Shepp"]`) |
| ReconFilterSize | REQUIRED | [number][] or [array][] of [numbers][] | Kernel size of post-recon filter (FWHM) in default units `"mm"`. |
| AttenuationCorrection | REQUIRED | [string][] | Short description of the attenuation correction method used. |
| ReconMethodImplementationVersion | RECOMMENDED | [string][] | Identification for the software used, such as name and version. |
| AttenuationCorrectionMethodReference | RECOMMENDED | [string][] | Reference paper for the attenuation correction method used. |
| ScaleFactor | RECOMMENDED | [array][] of [numbers][] | Scale factor for each frame. |
| ScatterFraction | RECOMMENDED | [array][] of [numbers][] | Scatter fraction for each frame (Units: 0-100%). |
| DecayCorrectionFactor | RECOMMENDED | [array][] of [numbers][] | Decay correction factor for each frame. |
| PromptRate | RECOMMENDED | [array][] of [numbers][] | Prompt rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |
| RandomRate | RECOMMENDED | [array][] of [numbers][] | Random rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |
| SinglesRate | RECOMMENDED | [array][] of [numbers][] | Singles rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------------------------------ | --------------------- | -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------- |
| AcquisitionMode | REQUIRED | [string][] | Type of acquisition of the PET data (for example, `"list mode"`) |
| ImageDecayCorrected | REQUIRED | [boolean][] | Boolean flag specifying whether the image data have been decay-corrected. |
| ImageDecayCorrectionTime | REQUIRED | [number][] | Point in time from which the decay correction was applied with respect to TimeZero in the default unit seconds. |
| ReconMethodName | REQUIRED | [string][] | Reconstruction method or algorithm (for example, `"3d-op-osem"`). |
| ReconMethodParameterLabels | REQUIRED | [array][] of [strings][] | Names of reconstruction parameters (for example, `["subsets", "iterations"]`) |
| ReconMethodParameterUnits | REQUIRED | [array][] of [strings][] | Unit of reconstruction parameters (for example, `["none", "none"]`). |
| ReconMethodParameterValues | REQUIRED | [array][] of [numbers][] | Values of reconstruction parameters (for example, `[21, 3]`) |
| ReconFilterType | REQUIRED | [string][] or [array][] of [strings][] | Type of post-recon smoothing (for example, `["Shepp"]`) |
| ReconFilterSize | REQUIRED | [number][] or [array][] of [numbers][] | Kernel size of post-recon filter (FWHM) in default units `"mm"`. |
| AttenuationCorrection | REQUIRED | [string][] | Short description of the attenuation correction method used. |
| ReconMethodImplementationVersion | RECOMMENDED | [string][] | Identification for the software used, such as name and version. |
| AttenuationCorrectionMethodReference | RECOMMENDED | [string][] | Reference paper for the attenuation correction method used. |
| ScaleFactor | RECOMMENDED | [array][] of [numbers][] | Scale factor for each frame. |
| ScatterFraction | RECOMMENDED | [array][] of [numbers][] | Scatter fraction for each frame (Units: 0-100%). |
| DecayCorrectionFactor | RECOMMENDED | [array][] of [numbers][] | Decay correction factor for each frame. |
| DoseCalibrationFactor | RECOMMENDED | [number][] | Multiplication factor used to transform raw data (in counts/sec) to meaningful unit (Bq/ml). Corresponds to DICOM Tag 0054,1322. |
| PromptRate | RECOMMENDED | [array][] of [numbers][] | Prompt rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |
| RandomRate | RECOMMENDED | [array][] of [numbers][] | Random rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |
| SinglesRate | RECOMMENDED | [array][] of [numbers][] | Singles rate for each frame (same units as `Units`, for example, `"Bq/mL"`). |

All reconstruction-specific parameters that are not specified, but one wants to include, should go into the `ReconMethodParameterValues` field.

Expand Down