README

## XTRACT xtract_divergence
# xtract-ing divergence metrics from blueprints


__  _______ ____      _    ____ _____   _ _
\ \/ /_   _|  _ \    / \  / ___|_   _|_| (_)_   __
 \  /  | | | |_) |  / _ \| |     | |/ _` | \ \ / /
 /  \  | | |  _ <  / ___ \ |___  | | (_| | |\ V /
/_/\_\ |_| |_| \_\/_/   \_\____| |_|\__,_|_| \_/

usage: xtract_divergence [-h] -bpa <CIFTI> -bpb <CIFTI> -out <folder> -masksa <GIFTI> <GIFTI> -masksb <GIFTI> <GIFTI> [-names <str> <str>] [-tract_list <list>] [-metric <str>]
            [-roi <path,<int>,[<int>,<int>,<int>],<str>] [-base_scalars <GIFTI> <GIFTI>] [-target_scalars <GIFTI> <GIFTI>] [-hemi <str>] [-ncores <int>]

xtract_divergence: Cross-brain divergence for divergence maps and translations

options:
  -h, --help            show this help message and exit
  -bpa <CIFTI>          Path to CIFTI blueprint. This is the base blueprint
  -bpb <CIFTI>          Path to CIFTI blueprint. This is the target blueprint: the space in which results will be saved
  -out <folder>         Path to output folder (plus any filename prefixes)
  -masksa <GIFTI> <GIFTI>
                        Path to GIFTI cortical left/right ROIs (excluding medial wall) of the base blueprint
  -masksb <GIFTI> <GIFTI>
                        Path to GIFTI cortical left/right ROIs (excluding medial wall) of the target blueprint
  -names <str> <str>    Names of base and target brains
  -tract_list <list>    Comma separated tract list defining the set of tracts to include - these must present in each brain
  -metric <str>         Kullback-Liebler (KLD, default), KLD without blueprint prep for backwards compatability (KLD_bias), or Jenson-Shannon (JSD) divergence
  -roi <path,<int>,[<int>,<int>,<int>],<str>
                        ROI or greyordinate coordinates (vertex index or voxel ijk indices) or CIFTI structure to calculate divergence wrt whole-brain. '-roi'
                        requires '-hemi' to be defined.
  -base_scalars <GIFTI> <GIFTI>
                        The scalar maps (left/right GIFTIs) to translate between brains
  -target_scalars <GIFTI> <GIFTI>
                        Scalar maps (left/right GIFTIs) in the target space
  -hemi <str>           If ROI prediction, the hemisphere of the ROI
  -ncores <int>         For JSD, you may specify single-core (default) or multi-core processing

Example call for human-to-macaque prediction of cortical MT+ ROI in the left hemisphere:
                xdiv -bpa human_BP.LR.dscalar.nii -bpb macaque_BP.LR.dscalar.nii
                    -masksa humam_atlasroi.L.shape.gii human_atlasroi.R.shape.gii
                    -masksb macaque_atlasroi.L.shape.gii macaque_atlasroi.R.shape.gii
                    -roi human_MTplus.L.shape.gii -hemi L

                    "-roi" flag options:
                            <path> to NIFTI/GIFTI binary mask. Mean blueprint in ROI used to calculate divergence to target whole-brain.
                            <int> single greyordinare vertex index. i.e. divergence between cortical location and whole-brain.
                            [<int>,<int>,<int>] ijk greyordinates. i.e. divergence between subcortical location and whole-brain.
                            <str> CIFTI subcortical structure. Options are those available as subcortical structures in the CIFTI convention CIFTI_STRUCTURE_* e.g. "CIFTI_STRUCTURE_THALAMUS_LEFT".
                            If no option supplied, will calculate dense (whole-brain to whole-brain) divergence.

KLD = Kullback-Leibler divergence (with addition of small value to blueprint for better behaved divergence maps)
KLD_bias = old-style KLD, has issues with zeros in blueprints
JSD = Jenson Shannon divergence