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.

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

[MISC] extract MRS institution info in separate table #1918

Merged
merged 2 commits into from
Aug 30, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 21 additions & 8 deletions src/modality-specific-files/magnetic-resonance-spectroscopy.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,8 @@ context of the academic literature.

!!! example "Example datasets"

Several [example MRS datasets](https://github.com/bids-standard/bids-examples/pull/425) have
been formatted using this specification and can be used for practical guidance when curating a new
dataset.
Several [example MRS datasets](https://github.com/bids-standard/bids-examples?tab=readme-ov-file#mrs) have
Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

PR has been merged

been formatted using this specification and can be used for practical guidance when curating a new dataset.

## MRS data

Expand Down Expand Up @@ -50,11 +49,13 @@ The `*.sdat` file contains either each coil-combined transient stored separately
or all transients summed into a signal average.
The `*.spar` file is a plaintext file describing acquisition parameters.
It is also possible to export raw data as `*.data`/`*.list` or DICOM files.
Siemens scanners allow data export in four formats: i) a proprietary DICOM-structured file known as IMA (`*.ima`);
ii) a conventional DICOM MR Spectroscopy Storage format (`*.dcm`); iii) RDA (`*.rda`),
a proprietary file format with a text-formatted header followed by the binary data points;
and iv) TWIX (`*.dat`), a proprietary file format designed for storing unreconstructed, unprocessed MRS data
from each individual coil element.
Siemens scanners allow data export in four formats:

1. a proprietary DICOM-structured file known as IMA (`*.ima`);
1. a conventional DICOM MR Spectroscopy Storage format (`*.dcm`);
1. RDA (`*.rda`), a proprietary file format with a text-formatted header followed by the binary data points;
1. TWIX (`*.dat`), a proprietary file format designed for storing unreconstructed, unprocessed MRS data from each individual coil element.

The IMA, DICOM MRS, and RDA formats are typically used to export reconstructed and processed data;
however, the sequence designer may choose to also allow the export of un-averaged transients
or data from individual coil elements.
Expand Down Expand Up @@ -153,6 +154,18 @@ A guide for using macros can be found at
-->
{{ MACROS___make_sidecar_table("mrs.MRSScannerHardware") }}

#### Institution information

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("mrs.MRSInstitutionInformation") }}

#### Sequence specifics

<!-- This block generates a metadata table.
Expand Down
10 changes: 8 additions & 2 deletions src/schema/rules/sidecars/mrs.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,20 @@

---
# MRS Common metadata fields
MRSScannerHardware:
MRSInstitutionInformation:
selectors:
- modality == "mrs"
- match(extension, "^\.nii(\.gz)?$")
fields:
InstitutionName: recommended
InstitutionAddress: recommended
InstitutionName: recommended
InstitutionalDepartmentName: recommended

MRSScannerHardware:
selectors:
- modality == "mrs"
- match(extension, "^\.nii(\.gz)?$")
fields:
Manufacturer: recommended
ManufacturersModelName: recommended
DeviceSerialNumber: recommended
Expand Down