Pulse sequence reconsideration (and fMRI techniques)

[UlrikeS91]

Offline discussion with @tgbugs and @lzehl about the general organization of pulse sequences: Start problem is that T1 and T2 are, in the physical sense not pulse sequences (e.g., https://radiopaedia.org/articles/mri-pulse-sequences-1 does not even list it under pulse sequences, and this quote "The MR signal intensity (S) produced using a spin echo sequence is proportional to the proton density (ρH), TR, T1, TE and T2, described by the equation S ∝ ρH [1-eTR/T1]e-TE/T2 4.")

Generic pulse sequences and contrast as separate parameter or have all combinations? - @tgbugs: rather split them

contrast agents (given to specimen or quality of the specimen) vs. weighting/contrast (algorithm that produces the contrasted image, hopefully making sense but theoretically could be applied to any kind of data) vs. pulse sequences (machine settings and which coil(s) were used and such, physically available data)

examples: contrast agent: oxygenated hemoglobin vs. deoxygenated hemoglobin pulse sequence: radio echo sequence, etc. MRI parameter weighting: T1, T2, T2star, proton-density, diffusion-weighted?, more?

Additionally some MRI technique should be reconsidered: functional MRI: fMRI as superclass for BOLD fMRI (blood oxygenation level dependent), VASO fMRI (vascular space occupancy) and ASL fMRI (arterial spin labeling) This is related to #128 (MRI as superclass with structural MRI and functional MRI)

diffusion-weighted imaging: is a protocol and not a single technique, should probably be sMRI + diffusion-weighted + some pulse sequence; what to do about these complex processes? should the "endpoint" be registered or not?

To Do:

• split weighting and sequences
• fix fMRI techniques

To Discuss:

• solution for the last point about complex processes

also related to #57

[lzehl]

For existing instances this means the following clean up:

Technique library > T1PulseSequence >>>> MRIWeighting library > T1weighting Technique library > T2PulseSequence >>>> MRIWeighting library > T2weighting ----> new controlledTerms schema MRIWeighting (related PR: https://github.com/openMetadataInitiative/openMINDS_controlledTerms/pull/479) ----> new Terminology instance "MRI weighting" ----> move T1/T2 into new terminology ----> add T2star, proton-density to new terminology

Technique library > spinEchoPulseSequence >>>> MRIPulseSequence library > spinEchoPulseSequence Technique library > echoPlanarPulseSequence >>>> MRIPulseSequence library > echoPlanarPulseSequence Technique library > gradientEchoPulseSequence >>>> MRIPulseSequence library > gradientEchoPulseSequence

Additional instance list will follow shortly

[UlrikeS91]

also related: https://github.com/openMetadataInitiative/openMINDS_instances/issues/130

[lzehl]

Additionally we should add / correct these pulse sequences (not finished yet with summary):

• spin echo pulse sequences
  • definition: An magnetic resonance imaging pulse sequence class which are all composed of a slice selective 90-degree pulse followed by one or more 180-degree refocusing pulses.
  • often combined with: T1-weighting, T2-weighting, proton density weighting
• inversion recovery pulse sequences
  • definition: An magnetic resonance imaging pulse sequence class which are all composed of a 180-degree radiofrequency pulse, followed by a slice selective 90-degree pulse, followed by one or more 180-degree refocusing pulses. The time elapsed between the preparatory 180-degree radiofrequency pulse and the 90-degree excitation (slice selection) radiofrequency pulse is termed time to inversion (TI). By choosing the appropriate TI, suppression of different tissues is possible.
  • often combined with: T1-weighting, T2-weighting
  • children (based on TI setting):
  • short tau inversion recovery pulse sequence (TI where signal of fat is zero)
  • fluid attenuated inversion recovery pulse sequence (TI where signal of cerebrospinal fluid is zero)
  • double inversion recovery pulse sequence (two inversion pulses with different TIs)
  • phase-sensitive inversion recovery pulse sequence (increases contrast according to tissue magnetization; precise TI less important)
• gradient echo sequences
• diffusion weighted sequences
• saturation recovery sequences
• echo-planar pulse sequences
• spiral pulse sequences