Method explanation =========== Here we give a brief overview of the hybrid data and method. Detailed methods can be found in the paper. Data -------- Our hyrbid orientations were created using the BigMac datset, which includes in vivo dMRI, postmortem dMRI and multi-contrast microscopy in a single macaque brain with the whole brain coverage. For more detailed information about the acquisition protocols, please refer to the `BigMac Documentation `_. This dataset is openly accessible. To create the hybrid FODs, we combined 3D diffusion MRI data with 2D microscopy data from BigMac. Specifically, we used postmortem diffusion-weighted MRI with a resolution of 0.6mm (b = 4 ms/μm2 with 128 gradient directions) and analyzed it using the Ball and Stick (BAS) model. For the 2D microscopy data we primarily used co-registered Polarised Light which estimates the primary fiber orientation per microscopy pixel by leveraging the birefringence of myelin. BigMac includes coronal PLI slices acquired every 350 microns along the anterior-posterior axis of the brain. Hybrid orientations were also generated from coronal slices stained for myelin and nissl bodies (see :doc:`Microscopy_contrasts` tab). .. figure:: ../html/_images/BigMacLogo.png :class: with-border | Hybrid FODs -------- How were the hybrid FODs generated? The in-plane orientation was provided by the microscopy data and the through-plane orientation (orientation going out of the microscopy plane) was approximmated by the diffusion MRI (see error matching process below). The in-plane and through-plane orientations were then combined to create the 3D hybrid orientation at the resolution of the microscopy. Next, these hybrid orientations were combined over a local neighbourhood (the size of a 0.4, 0.6 or 1mm voxel) to create a hybrid fibre orientation distribution (FOD). The hyrbid FOD was described using spherical harmonics. .. figure:: ../html/_images/fig13.jpg :width: 800 | Error based matching process -------- An error based matching process was used to select the through-plane orientation from the diffusion BAS model. The diffusion data was first analysed using the ball and stick model to estimate fibre populations per voxel (<3 fibre population each with 50 sample). For each microscopy pixel, we took the fibre orientation and compared it to the coregisterd diffusion outputs. The diffusion orientations were projected onto the microscopy plane to facilitate fair comparison. The in-plane orientations from both diffusiion MRI and microscopy were then compared. We selected the diffusion sample with the most similar in-plane orientation, and approximated the microscopy through plane angle with that from our diffusion sample. The prcess was then repeated. .. figure:: ../html/_images/fig14.jpg **Key references:** Howard, A.F.D., et al. An open resource combining multi-contrast MRI and microscopy in the macaque brain. Nature Communications 14, 4320 (2023). doi: 10.1038/s41467-023-39916-1