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![Oxford-MM-1 T1, T2 FLAIR, and DTI volumes][1]*Oxford-MM-1 T1, T2 FLAIR, and DTI volumes* ![Oxford-MM-1 T2 FLAIR overlayed with DTI volume][2]*Oxford-MM-1 T2 FLAIR overlayed with DTI volume* Online viewing (Firefox, or Google Chrome recommended): https://open.win.ox.ac.uk/pages/fsl/oxford-mm-templates/ Version 1 of our multimodal asymmetric template with its T1, T2 FLAIR and DTI volumes. It was constructed from **240 UK Biobank individuals uniformly sampled from the age range 50-55 years (50% female/male)**. We believe a template from this age range will be useful for a wealth of studies. Note that the template was **rigidly transformed to MNI space** to capture the population’s average brain shape and size, and avoid the introduction of unrepresentative scaling effects. When using this template please cite: **Arthofer, C., Smith, S.M., Jenkinson, M., Andersson, J., Lange, F. Multimodal MRI template construction from UK Biobank: Oxford-MM-0. (2021). Organisation for Human Brain Mapping (OHBM)** Several improvements to the pipeline include the use of: - weighted brain masks in T1 and DTI reference space, as well as in subjects' native DTI spaces to avoid the introduction of noise around - the brain FSL's epi_reg with BBR for more accurate rigid registrations between dMRI and T1 median (instead of mean) template - for the first few iterations to provide a better initialization non-defaced images Our general pipeline for template construction can be downloaded from https://git.fmrib.ox.ac.uk/cart/mm-template-construction. The images and transformations below are available as part of this package. Image dimensions are 182 x 218 x 182, voxel size is 1 mm isotropic and bit depth is 32 bit. | File | Description | |---|---| | `OMM-1_T1_head.nii.gz` | T1 whole-head volume | `OMM-1_T1_brain.nii.gz` | Brain-masked T1 volume | `OMM-1_T2_FLAIR_head.nii.gz` | T2 FLAIR whole-head volume | `OMM-1_T2_FLAIR_brain.nii.gz` | Brain-masked T2 FLAIR volume | `OMM-1_DTI_tensor.nii.gz` | 4D tensor volume | `OMM-1_DTI_FA.nii.gz` | Fractional anisotropy | `OMM-1_DTI_MD.nii.gz` | Mean diffusivity | `OMM-1_DTI_MO.nii.gz` | Mode of the anisotropy | `OMM-1_DTI_L1.nii.gz` | 1st eigenvalue | `OMM-1_DTI_L2.nii.gz` | 2nd eigenvalue | `OMM-1_DTI_L3.nii.gz` | 3rd eigenvalue | `OMM-1_DTI_V1.nii.gz` | 1st eigenvector | `OMM-1_DTI_V2.nii.gz` | 2nd eigenvector | `OMM-1_DTI_V3.nii.gz` | 3rd eigenvector | `OMM-1_T1_brain_mask_average.nii.gz` | Average (soft) brain mask by averaging over all resampled individual masks | `OMM-1_T1_brain_mask_weighted.nii.gz` | Weighted (soft) brain mask for registrations with whole-head images only; reduces regularisation in the brain compared to skull and surrounding regions (can be used as --mask_ref_scalar input to MMORF) | `OMM-1_DTI_mask_average.nii.gz` | Average brain mask for the DTI volume | `OMM-1_DTI_mask_weighted.nii.gz` | Weighted brain mask for the DTI volume to reduce the impact of noise around the edges of the brain during registrations (can be used as --mask_ref_tensor input to MMORF) | `transformations/FSL-MNI-152_to_oxford-mm-1_warp.nii.gz` | Combined warp (affine + nonlinear) to transform images (e.g., masks) from the space of FSL’s MNI 152 template to the space of the OMM-1 template. Directly compatible with FSL’s applywarp and vecreg function. | `transformations/oxford-mm-1_to_FSL-MNI-152_warp.nii.gz` | Combined warp (affine + nonlinear) to transform images (e.g., masks) from the space of the OMM-1 template to the space of FSL’s MNI 152 template. Directly compatible with FSL’s applywarp and vecreg function. DOI 10.17605/OSF.IO/S9GE4 Copyright, 2022, University of Oxford. All rights reserved [1]: https://git.fmrib.ox.ac.uk/fsl/oxford-mm-templates/-/raw/main/Oxford-MM-1/oxford-mm-1_overview.jpg [2]: https://git.fmrib.ox.ac.uk/fsl/oxford-mm-templates/-/raw/main/Oxford-MM-1/oxford-mm-1_T2+tensor.png
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