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Joel Williams
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Scans (dosma.scan_sequences)

DOSMA currently supports 4 MRI scan types:

  1. Quantitative DESS (qDESS)
  2. CubeQuant
  3. MAPSS
  4. UTE Cones

Each scan implements a subset of the following actions:

  1. Segment tissues from scan
  2. Interregister to register between lower resolution (moving) and higher resolution (target) scans
  3. Quantitative fitting for voxel-wise parameter maps.

Below we briefly discuss the different scan types and associated actions.

qDESS

Quantitative double echo in steady state (qDESS) is a high-resolution scan that has shown high efficacy for analytic T2 mapping :cite:`sveinsson2017simple`. Because of its high resolution, qDESS scans have been shown to be good candidates for automatic segmentation.

DOSMA supports both automatic segmentation and analytical T2 solving for qDESS scans. Automated segmentation uses pre-trained convolutional neural networks (CNNs).

CubeQuant (3D FSE)

Cubequant is a 3D fast-spin-echo (FSE) T1ρ-weighted sequence. Acquisitions between spin-locks are susceptible to motion, and as a result, volumes within the scan have to be registered to each other (i.e. intra-registered).

Moreover, CubeQuant scans often have lower resolution to increase SNR in practice. Because of the low-resolution, these scans are often registered to higher resolution target scans :cite:`jordan2014variability`.

By default, DOSMA intraregisters volumes acquired at different spin-locks to one another. This framework also supports both registration between scan types (interregistration) and T1ρ fitting.

Because registration is sensitive to the target scan type, different registration approaches may work better with different scan types. By default, the registration approaches are optimized to register CubeQuant scans to qDESS scans.

3D MAPSS (SPGR)

Magnetization‐prepared angle‐modulated partitioned k‐space spoiled gradient echo snapshots (3D MAPSS) is a spoiled gradient (SPGR) sequence that reduce specific absorption rate (SAR), increase SNR, and reduce the extent of retrospective correction of contaminating T1 effects :cite:`li2008vivo`.

The MAPSS sequence can be used to estimate both T1ρ and T2 quantitative values. Like CubeQuant scans, MAPSS scans must also be intraregistered to ensure alignment between all volumes acquired at different echos and spin-lock times.

DOSMA automatically performs intraregistration among volumes within the MAPSS scan. T2 and T1ρ fitting is also supported.

UTE Cones

Ultra-short echo time (UTE) Cones (or Cones) is a T2*-weighted sequence. In practice, many of these scans are low resolution.

DOSMA supports interregistration between Cones and other scan sequences; however, registration files are optimized for registration to qDESS. T2* fitting is also supported.