--- a
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+.. _scans:
+
+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.
+
+.. automodule::
+   dosma.scan_sequences
+
+.. autosummary::
+   :toctree: generated
+
+   dosma.scan_sequences.ScanSequence
+   dosma.scan_sequences.QDess
+   dosma.scan_sequences.CubeQuant
+   dosma.scan_sequences.Mapss
+   dosma.scan_sequences.Cones
+
+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) |T1rho|-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 |T1rho| 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 |T1rho| 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 |T1rho| fitting is also
+supported.
+
+
+UTE Cones
+--------------------------------------------------------------------------------
+Ultra-short echo time (UTE) Cones (or Cones) is a |T2star|-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. |T2star| fitting is also supported.
+
+
+.. Substitutions
+.. |T2| replace:: T\ :sub:`2`
+.. |T1| replace:: T\ :sub:`1`
+.. |T1rho| replace:: T\ :sub:`1`:math:`{\rho}`
+.. |T2star| replace:: T\ :sub:`2`:sup:`*`
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