From fc31bac9d47d4506bd65705b68a837fc317f289f Mon Sep 17 00:00:00 2001 From: markmikkelsen Date: Tue, 25 Oct 2022 19:41:56 -0400 Subject: [PATCH 001/218] First commit of bep022 into BIDS Adding and changing files to introduce MRS to the BIDS specification. --- mkdocs.yml | 1 + .../12-magnetic-resonance-spectroscopy.md | 102 ++++++++++++++++++ src/schema/objects/common_principles.yaml | 2 + src/schema/objects/datatypes.yaml | 4 + src/schema/objects/entities.yaml | 11 ++ src/schema/objects/modalities.yaml | 3 + src/schema/objects/suffixes.yaml | 24 +++++ src/schema/rules/entities.yaml | 1 + src/schema/rules/files/raw/mrs.yaml | 19 ++++ src/schema/rules/modalities.yaml | 3 + src/schema/rules/sidecars/mrs.yaml | 32 ++++++ 11 files changed, 202 insertions(+) create mode 100644 src/04-modality-specific-files/12-magnetic-resonance-spectroscopy.md create mode 100644 src/schema/rules/files/raw/mrs.yaml create mode 100644 src/schema/rules/sidecars/mrs.yaml diff --git a/mkdocs.yml b/mkdocs.yml index 0bb0d57ede..765955ded1 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -66,6 +66,7 @@ nav: - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md - Microscopy: 04-modality-specific-files/10-microscopy.md - Near-Infrared Spectroscopy: 04-modality-specific-files/11-near-infrared-spectroscopy.md + - Magnetic Resonance Spectroscopy: 04-modality-specific-files/12-magnetic-resonance-spectroscopy.md - Derivatives: - BIDS Derivatives: 05-derivatives/01-introduction.md - Common data types and metadata: 05-derivatives/02-common-data-types.md diff --git a/src/04-modality-specific-files/12-magnetic-resonance-spectroscopy.md b/src/04-modality-specific-files/12-magnetic-resonance-spectroscopy.md new file mode 100644 index 0000000000..e1b828b743 --- /dev/null +++ b/src/04-modality-specific-files/12-magnetic-resonance-spectroscopy.md @@ -0,0 +1,102 @@ +# Magnetic Resonance Spectroscopy + +Support for Magnetic Resonance Spectroscopy (MRS) was developed as a +[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals). +Please see [Citing BIDS](../01-introduction.md#citing-bids) +on how to appropriately credit this extension when referring to it in the +context of the academic literature. + +Several [example MRS datasets](https://github.com/bids-standard/bids-examples#mrs-datasets) +have been formatted using this specification and can be used for practical guidance when curating a new dataset. + +## MRS data + + +{{ MACROS___make_filename_template( + "raw", + datatypes=["mrs"], + suffixes=["svs", "mrsi", "ref", "unloc"]) +}} + +Each manufacturer has its own file format (sometimes multiple formats) for exporting MRS data from the scanner console for offline processing. +GE exports a P-file that stores unprocessed, un-coil-combined data with metadata embedded in a proprietary data header. +Philips has multiple export formats, the most common being the SDAT/SPAR format. +The `*.sdat` file contains either each coil-combined average stored separately or all averages 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 and DICOM files. +Siemens scanners allow data export in 4 formats: +1) a proprietary DICOM structured file known as IMA (`*.ima`); +2) a conventional DICOM MR Spectroscopy Storage format (`*.dcm`); +3) RDA (`*.rda`) a proprietary file format with a text formatted header followed by the binary data points and +4) TWIX (`*.dat`) a proprietary file format designed for storing unreconstructed and unprocessed MRS data from each individual coil element. +IMA, DICOM MRS and RDA formats are typically used to export the 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. +Contrarily, Bruker stores two binary files: one file stores each average separately, +while the other file stores the sum of the average. +Bruker stores the sequence, voxel position, and voxel orientation; +other metadata are stored in a separate plaintext file. + +Due to the diversity in manufacturer MRS data formats, we define a single standardized format for storing MRS data. +For compliance, data MUST be converted to the [NIfTI-MRS format](https://onlinelibrary.wiley.com/doi/10.1002/mrm.29418) (`*.nii.gz`), +a data format based on the NIfTI framework designed to accommodate the nuances of raw MRS data. +All necessary information to parse this `*.nii.gz` file (e.g., spectrometer frequency, +echo time, repetition time, etc.) will be stored in a sidecar JSON (`*.json`) file. +Conversion of proprietary MRS file formats to NIfTI-MRS and extraction of +some (but not all) BIDS-compliant metadata can be performed using [spec2nii](https://github.com/wtclarke/spec2nii). +Note that the "rawness" of data stored in the NIfTI-MRS file will depend +on what format the source data are in. +It is RECOMMENDED that users export their source data in an appropriately raw format +prior to conversion. + +For MRSI data, "raw" signifies spatially reconstructed data +(i.e., in image space rather than (k,t)-space), +given the complexity and diversity of sampling approaches. +NIfTI-MRS is not designed to store data that has not been spatially reconstructed. + +### Single-voxel spectroscopy and MRS imaging + +A major distinction between MRS acquisitions is whether the acquisition technique probes +spectral information from a single volume (single-voxel spectroscopy, SVS) +or encodes this information along 1, 2 or 3 spatial dimensions +resulting in multiple subvolumes (MRS imaging, MRSI). +To avoid confusion, a suffix MUST be included in the filename and MUST be denoted as `svs` or `mrsi`. +For cases where localization is not used, the suffix `unloc` SHOULD be used. + +Furthermore, it is common to acquire an additional MRS dataset that may serve +as a reference for scaling metabolite levels (e.g., to obtain concentrations) +and/or aid preprocessing steps such as eddy-current correction, RF coil combination, phasing, and frequency calibration. +This could be either an external reference (e.g., a phantom or a synthetic signal) or, +more typically, an internal tissue water reference. +For such datasets, the suffix ref MUST be used. +Should multiple references exist for a given dataset, the user MAY use the `acq-