Multi-modal brain MR image simulation data

The simulated Brain MR image database is based on the Bloch equations analytical solutions for Earnst angle solution, spin echo signal, and inversion recovery spin echo signal for brain MRI. A realistic multi-modal simulation framework is designed by incorporating patient-specific phantoms and Bloch equations-based analytical solutions for fast and accurate MR image simulations. The framework generates realistic-looking images with controllable imaging parameters such as SNR, TR, TE, and flip angle as well as MR tissue properties such as T1, T2, and proton density. A diverse brain image database with variable image appearances is simulated using the framework.

To create our virtual population, we change three categories of parameters: i) anatomical parameters, ii) MR tissue properties and iii) imaging parameters. To create virtual subjects with natural variable anatomical representation, we utilized the self-derived patient specific phantoms (20-class brain classification labels acquired on real HCP T1w 3D brain MRI data). We vary T1 and T2 relaxation times and proton density for the 20 tissues visible in the field of view. We slightly alter repetition time (TR), echo time (TE) and flip angle for gradient echo, spin echo and inversion recovery sequence. Complex Gaussian noise is added in k-space to achieve variations in signal-to-noise-ratios. Tukey window filtering in the frequency domain (k-space) is applied to avoid ringing artifacts before FFT reconstruction. The images and labels are stored in NIFTI format.

The first version of the multi-modal simulated database for Brain MR images, includes 200 patient specific virtual subjects with variable parameters. Each subject is provided with its corresponding ground truth label map including all simulated tissue types; Gray Matter, White Matter, cerebellum, corpus callosum, hippocampus, brainstem, pons, amygdala, fornix, putamen, thalamus, globus pallidus, caudate nucleus and accumbens, third ventricle, lateral ventricle, CSF and septum pellicudum. A detailed description of the tissue types and label information for simulated tissues is provided as a separate text file named label_info.txt.