White matter anisotropy
-
Hello
i was able to use the trial version of the software and finally we bought it and now we want to perform TI simulation with anisotropic properties of the whitte matter and in the midbrain.
the 2 screenshot was a simulation performed by Antonino Cassara and i would like to reproduce the simulation he sent us but i don't have access to the anisotropic data.
how to have access to these files ?
-
Hello
i was able to use the trial version of the software and finally we bought it and now we want to perform TI simulation with anisotropic properties of the whitte matter and in the midbrain.
the 2 screenshot was a simulation performed by Antonino Cassara and i would like to reproduce the simulation he sent us but i don't have access to the anisotropic data.
how to have access to these files ? @pastis the anisotropic conductivity is subject specific, and could be evaluated from diffusion weighted images (based on Tuch et al.). Sim4life has an implementation to compute this, but we recently noticed a bug in 6.2 which has been fixed for the 7.0 branch. We will include a python tutorial for this workflow in the 7.0 release.
Alternatively, Sim4Life allows to generate anisotropic conductivity tensor fields given a field that encodes the main directionality (i.e. direction of largest eigenvector). This can be useful for tissues where there is a known directionality, e.g. along some elongated structure.
-
@pastis the anisotropic conductivity is subject specific, and could be evaluated from diffusion weighted images (based on Tuch et al.). Sim4life has an implementation to compute this, but we recently noticed a bug in 6.2 which has been fixed for the 7.0 branch. We will include a python tutorial for this workflow in the 7.0 release.
Alternatively, Sim4Life allows to generate anisotropic conductivity tensor fields given a field that encodes the main directionality (i.e. direction of largest eigenvector). This can be useful for tissues where there is a known directionality, e.g. along some elongated structure.
-
The latest 8.2 release includes a tutorial Jupyter notebook (
tutorial_dti_conductivity.ipynb) demonstrating how to import the DTI, convert it to anisotropic conductivity, and assign it to a low-frequency simulation via Python.@bryn this is the list of the tutorials that I found in C:\Users\Documents\ZMT\Sim4Life\8.2\Documentation\Tutorials\Tutorial Scripts: tutorial_acoustic_seft
tutorial_emftd_dipole_antenna_broadband
tutorial_emftd_dipole_antenna_harmonic
tutorial_emftd_ieee_scc34_benchmark
tutorial_emftd_microstrip_fed_patch_ant
tutorial_emftd_mri_single_loop_coil
tutorial_emftd_mri_system_and_lead_pa
tutorial_emftd_plane_wave
tutorial_emftd_pt3Coil
tutorial_emftd_SAHeadPhone
tutorial_emftd_gradient_coil
tutorial_emftd_parallel_plate
tutorial_emftd_transcranial_magnetic_stim
tutorial_emfl_two_metallic_spheres
tutorial_emfl_unstructured_neuron_electrodes
tutorial_head_segmentation_10_10_system
tutorial_neuron_hoc
tutorial_neuron_monopole
tutorial_neuron_neural_networks
tutorial_petri_dish_T1_fields
tutorial_thermal_heated_brain
tutorial_tier3_simulation -
It is a Jupyter notebook:
C:\Users\Public\Documents\ZMT\Sim4Life\8.2\Documentation\Example Notebooks
