diff --git a/src/modality-specific-files/magnetic-resonance-spectroscopy.md b/src/modality-specific-files/magnetic-resonance-spectroscopy.md index 19e4868a48..bc3c94be4c 100644 --- a/src/modality-specific-files/magnetic-resonance-spectroscopy.md +++ b/src/modality-specific-files/magnetic-resonance-spectroscopy.md @@ -47,9 +47,9 @@ GE exports a P-file (`*.7`) that stores unprocessed, un-coil-combined data with 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 transient stored separately -or all transient summed into a signal average. +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` and DICOM files. +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; @@ -58,10 +58,10 @@ 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. -Contrarily, Bruker stores two binary files: one file stores each transient separately, +Bruker data are are exported as two binary files: one file stores each transient separately, while the other stores the sum of the transients. -Bruker stores the sequence name, voxel position, voxel orientation, and other metadata in a separate plaintext file. -These files are considered source data and, if present, MUST be stored in the +A separate plaintext file stores the sequence name, voxel position, voxel orientation, and other metadata. +All of these files are considered source data and, if present, MUST be stored in the [`sourcedata`](../common-principles.md#source-vs-raw-vs-derived-data) directory. ### Single-voxel spectroscopy and MRS imaging @@ -100,33 +100,33 @@ Users are free to choose any label they wish as long as they are consistent acro and sessions and use only legal label characters. If used, the chosen label SHOULD also be described in the `PulseSequenceType` field in the sidecar JSON file. -| **Name** | **`label`** | **Description** | -| ------------------------------------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| PRESS | press | A double spin-echo sequence that achieves spatial localization by employing three slice-selective RF pulses: 90°–180°–180°–acq. | -| STEAM | steam | A stimulated-echo sequence that uses three 90° slice-selective pulses for spatial localization. | -| LASER | laser | LASER uses three pairs of slice-selective 180° adiabatic full-passage (AFP) refocusing pulses for localization. These are preceded by a non-slice-selective adiabatic half-passage (AHP) excitation pulse. | -| sLASER | slaser | sLASER is a modification of LASER where the AHP and first pair of AFP pulses are replaced with a non-adiabatic slice-selective 90° excitation pulse, typically employed to reduce the minimum TE. | -| SPECIAL | special | SPECIAL is a two-shot experiment. In the first shot, a pre-excitation slice-selective 180° AFP inversion pulse precedes a spin-echo acquisition with slice selection (90°–180°–acq). In the second shot, the adiabatic pulse is not applied. The 3D localized signal is derived by subtracting the two shots. | -| MEGA | mega | MEGA is a spectral editing technique that applies narrowband frequency-selective 180° pulses to refocus *J*-coupled spins at a specific frequency without affecting the spins of metabolites with resonances beyond the frequency range. Applying these pulses in alternating scans (for example, edit ON and edit OFF) and then subtracting the ON/OFF pairs results in a *J*-difference-edited spectrum that removes the unedited signals leaving only those signals that were affected by the editing pulses. | -| HERMES | hermes | HERMES is an extension of MEGA editing whereby the two-step experiment becomes a four-step experiment. This permits multiple metabolites to be edited in a multiplexed manner. By employing Hadamard combination of the four edited sub-spectra, HERMES can reveal several metabolites unambiguously. | -| HERCULES | hercules | HERCULES is a different flavor of HERMES that targets more metabolites using the same four-step experiment. | -| Multiple quantum coherence (MQC) editing | mqc | MQC editing targets *J*-coupled resonances by selecting desired coherence pathways using MQ gradients and frequency-selective RF pulses. | -| Localized correlation spectroscopy (L-COSY) | lcosy | L-COSY is a 2D MRS technique whereby one of the interpulse durations is changed sequentially. A 2D Fourier transform produces a 2D spectrum that displays singlets on the diagonal and *J*-coupled metabolites on the off-diagonal, with the offsets equal to the *J*-coupling constants. | -| *J*-resolved spectroscopy | j | Another 2D technique, where in a *J*-resolved acquisition, a series of transients are collected at different TEs. A 2D Fourier transform is applied to generate a 2D spectrum where one dimension characterizes both chemical shift and *J*-coupling and the other only *J*-coupling. | -| Diffusion-weighted (DW) spectroscopy | dw | The diffusion of intracellular metabolites can be characterized using DW spectroscopy. In such acquisitions, the strength of gradients in a conventional MRS sequence is modulated to sensitize the metabolite signals to diffusion. | -| FID spectroscopy | fid | FID spectroscopy is a pulse-acquire acquisition where an excitation pulse is followed by direct acquisition of the FID. This approach is most often used in MRSI (that is, FID-MRSI) when combined with slice- or slab-selection. | -| Metabolite-cycled (MC) spectroscopy | mc | MC spectroscopy involves the use of asymmetric adiabatic inversion of the upfield and downfield parts of the MR spectrum, allowing for simultaneous acquisition of water and metabolite spectra. | -| Spin-echo spectroscopy | spinecho | An MRS experiment whereby the MR signal is detected using a spin-echo acquisition: for example, 90°–180°–acq. | - -Each `