Synthetic MRI Signal Standardization: Application to Multi-atlas Analysis

Abstract

From the image analysis perspective, a disadvantage of MRI is the lack of image intensity standardization. Differences in coil sensitivity, pulse sequence and acquisition parameters lead to very different mappings from tissue properties to image intensity levels. This presents challenges for image analysis techniques because the distribution of image intensities for different brain regions can change substantially from scan to scan. Though intensity correction can sometimes alleviate this problem, it fails in more difficult scenarios in which different types of tissue are mapped to similar gray levels in one scan but different intensities in another. Here, we propose using multi-spectral data to create synthetic MRI scans matched to the intensity distribution of a given dataset using a physical model of acquisition. If the multi-spectral data are manually annotated, the labels can be transfered to the synthetic scans to build a dataset-tailored gold standard. The approach was tested on a multi-atlas based hippocampus segmentation framework using a publicly available database, significantly improving the results obtained with other intensity correction methods.

Multi-atlas segmentation of biomedical images: A survey

“…Many methods have been developed to parcellate the whole brain, segmenting it into a large number of regions (Aljabar et al, 2008; Babalola et al, 2009; Fonov et al, 2012; Han et al, 2009; Heckemann et al, 2010, 2011; Keihaninejad et al, 2010; Kotrotsou et al, 2014; Svarer et al, 2005; Wang et al, 2012; Ledig et al, 2014), while other studies have focused on small sets or individual ROIs, such as the caudate nucleus (van Rikxoort et al, 2007b); the cerebellum (Park et al, 2014; Van Der Lijn et al, 2012; Weier et al, 2014); the amygdala (Hanson et al, 2012; Klein-Koerkamp et al, 2014); the corpus callosum (Ardekani et al, 2014; Gao et al, 2014; Meyer, 2014); the striatum (Janes et al, 2014); the subthalamic nucleus, red nucleus and substantia nigra (Xiao et al, 2014b,a); the ventricles (Chou et al, 2008; Raamana et al, 2014); and, most notably, the hippocampus, which has attracted much attention due to its association with dementia and Alzheimer’s disease (Akhondi-Asl et al, 2010; Bishop et al, 2010; Clerx et al, 2013; Hammers et al, 2007; Iglesias et al, 2010; Kim et al, 2012; Leung et al, 2010; Pipitone et al, 2014; Pluta et al, 2012; Raamana et al, 2014; van der Lijn et al, 2008; Van Der Lijn et al, 2012; Winston et al, 2013; Wolz et al, 2010b; Yushkevich et al, 2010; Platero et al, 2014; Ta et al, 2014). …”

Extended Modality Propagation: Image Synthesis of Pathological Cases

“…Given MR scanner parameters such as echo time and relaxation time, a discreteevent simulation model [8]- [10] describes the dynamics of magnetization vectors, at each spatial position, according to Bloch equations [11]. Such numerical simulations are computationally expensive, except for specific cases for which there exists a closed-form solution to Bloch equations, such as for spin-echo or gradient-echo MR sequences [8], [12], [13].…”

“…However, it requires the knowledge of tissue-specific biophysical properties [8], which are poorly referenced in the literature for glioblastoma compartments. The second strategy does not rely on the definition of tissues: biophysical properties are specified voxel-wise, after an estimation from several MR scans obtained in a short time-frame with a very strict acquisition protocol (quantitative MRI or relaxometry), or by optimization methods [12], [13]. This strategy does not allow to generate synthetic images on virtual patients.…”

Inter‐station intensity standardization for whole‐body MR data

“…Jäger and Hornegger developed a method that can be used for standardizing image intensities between two different whole‐body scans. Iglesias et al and Jog et al presented approaches that are considerably different from all the other methods as they perform standardization based on MR physics acquisition equations.…”