Corticospinal Tract Analysis in Brain MRI

Several pre-processing steps were taken prior to analysis of the brain MRI data, which are described in further detail in Appendix 5. These included conversion from DICOM to NIFTI-1 using dcm2niix, followed by correction of eddy current and motion artifact in the diffusion volumes through use of the FSL TOPUP/EDDY algorithm.
Manual segmentation of regions of interest corresponding to the location of the corticospinal tract (CST) was performed bilaterally in the: corona radiata, posterior limb of internal capsule (PLIC), and cerebral peduncles. The corona radiata slice was selected to be one slice above the top of the ventricles; the PLIC slice was selected at the level of the foramina of Munro; and the cerebral peduncle slice was selected one slice below the bottom of the thalami (Figure 5). The volumetric T1 scan and the color FA maps were used as guidance to identify the corticospinal tract at these levels, with reference to a detailed white matter atlas (38 ).
Descriptive statistics were calculated in DSI studio and data describing the fractional anisotropy were obtained from the cross-sectional regions of interest corresponding to the tract at these three separate locations. The affected side data was normalized against the unaffected side to account for any background variation.