Toblerone

Surface-based analysis tools

Installation

Cython and numpy need to be installed prior to running pip:

python -m pip install cython numpy
python -m pip install toblerone

Usage from command line

Run toblerone -h to see available commands and help info.

Usage from Python: PV estimation

Toblerone can estimate partial volumes (PVs) across the brain using surface segmentations (for example, those from FreeSurfer and FSL FIRST). This can be used as a direct replacement for tools such as FSL FAST. The following functions are available in toblerone.pvestimation:

  • toblerone.pvestimation.estimation.cortex(): estimate PVs for one/both hemispheres of the cortex
  • toblerone.pvestimation.estimation.structure(): estimate PVs for a structure delineated by a single surface, eg thalamus
  • toblerone.pvestimation.estimation.all(): estimate PVs across the whole brain, including subcortical structures identified by FSL FIRST

Parial volume correction

Toblerone has been integrated with oxasl to provide PV correction via the spatial Variational Bayesian method. See [oxasl](#https://github.com/ibme-qubic/oxasl) and [oxasl_surfpvc](#https://github.com/ibme-qubic/oxasl_surfpvc).

Usage from Python: PV estimation

This is work in progress.

Indices and tables