Surface-based analysis tools
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¶
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.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).