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Merge pull request #623 from sappelhoff/order
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[FIX] arrays of 3D coordinates MUST supply numeric values in x, y, z order
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sappelhoff authored Oct 3, 2020
2 parents d3ed5ff + 2cede62 commit 113b724
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16 changes: 8 additions & 8 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -30,15 +30,15 @@ Example for `ReceiveCoilActiveElements`:

For Siemens, coil channels are typically not activated/selected individually,
but rather in pre-defined selectable "groups" of individual channels,
and the list of the "groups" of elements that are active/selected in any
and the list of the "groups" of elements that are active/selected in any
given scan populates the `Coil String` entry in Siemens' private DICOM fields
(for example, `HEA;HEP` for the Siemens standard 32 ch coil
(for example, `HEA;HEP` for the Siemens standard 32 ch coil
when both the anterior and posterior groups are activated).
This is a flexible field that can be used as most appropriate for a given
This is a flexible field that can be used as most appropriate for a given
vendor and coil to define the "active" coil elements.
Since individual scans can sometimes not have the intended coil elements selected,
it is preferable for this field to be populated directly from the DICOM
for each individual scan, so that it can be used as a mechanism for checking
it is preferable for this field to be populated directly from the DICOM
for each individual scan, so that it can be used as a mechanism for checking
that a given scan was collected with the intended coil elements selected

### Sequence Specifics
Expand Down Expand Up @@ -102,9 +102,9 @@ first "effective" echo and the center of the last "effective" echo.

Useful for multimodal co-registration with MEG, (S)EEG, TMS, etc.

| **Key name** | **Requirement level** | **Data type** | **Description** |
|-------------------------------|-----------------------|--------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| AnatomicalLandmarkCoordinates | RECOMMENDED | [object][] of [arrays][] | Key:value pairs of any number of additional anatomical landmarks and their coordinates in voxel units (where first voxel has index 0,0,0) relative to the associated anatomical MRI, (for example, `{"AC": [127,119,149], "PC": [128,93,141], "IH": [131,114,206]}, or {"NAS": [127,213,139], "LPA": [52,113,96], "RPA": [202,113,91]}`). |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ----------------------------- | --------------------- | ------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| AnatomicalLandmarkCoordinates | RECOMMENDED | [object][] of [arrays][] | Key:value pairs of any number of additional anatomical landmarks and their coordinates in voxel units (where first voxel has index 0,0,0) relative to the associated anatomical MRI (for example, `{"AC": [127,119,149], "PC": [128,93,141], "IH": [131,114,206]}`, or `{"NAS": [127,213,139], "LPA": [52,113,96], "RPA": [202,113,91]}`). Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order. |

### Institution information

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24 changes: 12 additions & 12 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -298,12 +298,12 @@ MEG and EEG sensors:

Head localization coils:

| **Key name** | **Requirement level** | **Data type** | **Description** |
|-------------------------------------|-----------------------|--------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| HeadCoilCoordinates | OPTIONAL | [object][] of [arrays][] | Key:value pairs describing head localization coil labels and their coordinates, interpreted following the `HeadCoilCoordinateSystem`, for example, {`NAS`: `[12.7,21.3,13.9]`, `LPA`: `[5.2,11.3,9.6]`, `RPA`: `[20.2,11.3,9.1]`}. Note that coils are not always placed at locations that have a known anatomical name (for example, for Elekta, Yokogawa systems); in that case generic labels can be used (for example, {`coil1`: `[12.2,21.3,12.3]`, `coil2`: `[6.7,12.3,8.6]`, `coil3`: `[21.9,11.0,8.1]`}). |
| HeadCoilCoordinateSystem | OPTIONAL | [string][] | Defines the coordinate system for the coils. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If "Other", provide definition of the coordinate system in `HeadCoilCoordinateSystemDescription`. |
| HeadCoilCoordinateUnits | OPTIONAL | [string][] | Units of the coordinates of `HeadCoilCoordinateSystem`. MUST be `m`, `cm`, or `mm`. |
| HeadCoilCoordinateSystemDescription | OPTIONAL | [string][] | Freeform text description or link to document describing the Head Coil coordinate system system in detail. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ----------------------------------- | --------------------- | ------------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| HeadCoilCoordinates | OPTIONAL | [object][] of [arrays][] | Key:value pairs describing head localization coil labels and their coordinates, interpreted following the `HeadCoilCoordinateSystem` (for example, `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}`). Note that coils are not always placed at locations that have a known anatomical name (for example, for Elekta, Yokogawa systems); in that case generic labels can be used (for example, `{"coil1": [12.2,21.3,12.3], "coil2": [6.7,12.3,8.6], "coil3": [21.9,11.0,8.1]}`). Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order. |
| HeadCoilCoordinateSystem | OPTIONAL | [string][] | Defines the coordinate system for the coils. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If "Other", provide definition of the coordinate system in `HeadCoilCoordinateSystemDescription`. |
| HeadCoilCoordinateUnits | OPTIONAL | [string][] | Units of the coordinates of `HeadCoilCoordinateSystem`. MUST be `m`, `cm`, or `mm`. |
| HeadCoilCoordinateSystemDescription | OPTIONAL | [string][] | Freeform text description or link to document describing the Head Coil coordinate system system in detail. |

Digitized head points:

Expand All @@ -322,12 +322,12 @@ Anatomical MRI:

Anatomical landmarks:

| **Key name** | **Requirement level** | **Data type** | **Description** |
|-----------------------------------------------|-----------------------|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| AnatomicalLandmarkCoordinates | OPTIONAL | [object][] of [arrays][] | Key:value pairs of the labels and 3-D digitized locations of anatomical landmarks, interpreted following the `AnatomicalLandmarkCoordinateSystem`, for example, {"NAS": `[12.7,21.3,13.9]`, "LPA": `[5.2,11.3,9.6]`, "RPA": `[20.2,11.3,9.1]`}. |
| AnatomicalLandmarkCoordinateSystem | OPTIONAL | [string][] | Defines the coordinate system for the anatomical landmarks. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `AnatomicalLandmarkCoordinateSystemDescription`. |
| AnatomicalLandmarkCoordinateUnits | OPTIONAL | [string][] | Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`. MUST be `m`, `cm`, or `mm`. |
| AnatomicalLandmarkCoordinateSystemDescription | OPTIONAL | [string][] | Freeform text description or link to document describing the Head Coil coordinate system system in detail. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| --------------------------------------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| AnatomicalLandmarkCoordinates | OPTIONAL | [object][] of [arrays][] | Key:value pairs of the labels and 3-D digitized locations of anatomical landmarks, interpreted following the `AnatomicalLandmarkCoordinateSystem` (for example, `{"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}`. Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order. |
| AnatomicalLandmarkCoordinateSystem | OPTIONAL | [string][] | Defines the coordinate system for the anatomical landmarks. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `AnatomicalLandmarkCoordinateSystemDescription`. |
| AnatomicalLandmarkCoordinateUnits | OPTIONAL | [string][] | Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`. MUST be `m`, `cm`, or `mm`. |
| AnatomicalLandmarkCoordinateSystemDescription | OPTIONAL | [string][] | Freeform text description or link to document describing the Head Coil coordinate system system in detail. |

It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical
landmarks for co-registration of MEG with structural MRI are stored in the
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