Compare to other modalities' pipelines

docs/comparisons.rst

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+##########################
+Comparisons to other tools
+##########################
+
+***********************************
+Comparisons to other dMRI pipelines
+***********************************
+
+Other pipelines for preprocessing DWI data are currently being developed.
+Below are tables comparing their current feature sets.
+
+* `Tractoflow <https://doi.org/10.1016/j.neuroimage.2020.116889>`_
+* `PreQual <https://doi.org/10.1101/2020.09.14.260240>`_
+* `MRtrix3_connectome <https://github.com/BIDS-Apps/MRtrix3_connectome>`_
+* `dMRIPrep <https://github.com/nipreps/dmriprep>`_
+
+
+Supported Sampling Schemes
+==========================
+
+.. list-table::
+   :header-rows: 1
+
+   * -
+     - QSIPrep
+     - Tractoflow
+     - PreQual
+     - MRtrix3_connectome
+     - dMRIPrep
+   * - Single Shell
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+   * - Multi Shell
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+   * - Cartesian
+     - ✔
+     - ✘
+     - ✘
+     - ✘
+     - ✘
+   * - Random (Compressed Sensing)
+     - ✔
+     - ✘
+     - ✘
+     - ✘
+     - ✘
+
+
+Preprocessing
+=============
+
+.. list-table::
+   :header-rows: 1
+
+   * -
+     - QSIPrep
+     - Tractoflow
+     - PreQual
+     - MRtrix3_connectome
+     - dMRIPrep
+   * - BIDS App
+     - ✔
+     - ✔
+     - ✘
+     - ✔
+     - ✔
+   * - Gradient direction sanity check
+     - Q-form matching
+     - ✘
+     - ``dwigradcheck``
+     - ✘
+     - ✘
+   * - Workflow management
+     - NiPyPe
+     - NextFlow
+     - Custom
+     - Custom
+     - NiPyPe
+   * - MP-PCA denoising
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+     - ✘
+   * - Patch2self denoising
+     - ✔
+     - ✘
+     - ✘
+     - ✘
+     - ✘
+   * - Gibbs unringing
+     - ``mrdegibbs``
+     - ``mrdegibbs`` (disabled)
+     - ``mrdegibbs`` (disabled)
+     - ``mrdegibbs``
+     - ✘
+   * - B1 bias field correction
+     - N4
+     - N4
+     - N4
+     - N4
+     - ✘
+   * - Automatic distortion group concatenation
+     - ✔
+     - ✘
+     - ✘
+     - ✔
+     - ✘
+   * - T1w brain extraction
+     - ANTs
+     - ANTs
+     - ✘
+     - ✘
+     - ANTs
+   * - Intensity normalization
+     - scaled by *b*=0 means
+     - *b*=0 mean set to 1000
+     - ✘
+     - ``mtnormalize``
+     - ✘
+   * - b=0 to T1w coregistration
+     - ANTs linear registration
+     - ANTs Non-Linear SyN
+     - ✘
+     - ``mrregister``
+     - FSL BBR
+   * - Head Motion Correction (shelled schemes)
+     - ``eddy``
+     - ``eddy``
+     - ``eddy``
+     - ``eddy``
+     - ✘
+   * - Head Motion Correction (Cartesian / Random Schemes)
+     - SHORELine
+     - ✘
+     - ✘
+     - ✘
+     - ✘
+   * - PEPOLAR EPI distortion correction
+     - ``TOPUP``
+     - ``TOPUP``
+     - ``TOPUP``
+     - ``TOPUP``
+     - ``TOPUP``
+   * - GRE Fieldmap EPI distortion correction
+     - ✔
+     - ✘
+     - ✘
+     - ✘
+     - ✔
+   * - Fieldmapless Distortion Correction
+     - PE-Direction SyN
+     - ✘
+     - Non-Linear registration
+     - SyN b0-DISCO
+     - PE-Direction SyN
+   * - T1w-based Normalization
+     - ANTs (SyN)
+     - ✘
+     - ✘
+     - ✘
+     - ANTs (SyN)
+   * - HTML Report
+     - ✔
+     - ✘
+     - ✔
+     - ✘
+     - ✔
+   * - Containerized
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+     - ✔
+
+
+Quality Control
+===============
+
+.. list-table::
+   :header-rows: 1
+
+   * -
+     - QSIPrep
+     - Tractoflow
+     - PreQual
+     - MRtrix3_connectome
+   * - Automated methods boilerplate
+     - ✔
+     - ✘
+     - ✘
+     - ✘
+   * - HTML Preprocessing Report
+     - `NiWorkflows-based <preprocessing.html#visual-reports>`_
+     - ✘
+     - Custom
+     - EddyQuad
+   * - HTML Reconstruction Report
+     - NiWorkflows-based
+     - ✘
+     - Custom
+     - ✘
+
+
+***********************************
+QSIPrep versus other modality preps
+***********************************
+
+Diffusion processing has idiosyncrasies that may confuse users who are used to
+working with other modalities.
+This section is designed to orient users who are familiar with pipelines like fMRIPrep and ASLPrep.
+
+
+Output spaces
+=============
+
+With fMRIPrep and other, similar pipelines, the user defines any output spaces they want,
+and the workflow will write out preprocessed data in those spaces.
+With QSIPrep, the pipeline will write out the preprocessed DWI data in a native anatomical space-
+typically the T1w space, aligned to the ACPC.
+The "output spaces" in this case will be provided as transforms from the T1w space to the
+desired output space.
+It is then up to the reconstruction pipeline (typically QSIRecon) to apply these transforms to the
+preprocessed DWI data to get reconstructed outputs in the requested spaces.
+
+
+Output resolution
+=================
+
+
+Concatenation across runs
+=========================