Similar protocols

Protocol publication

[…]  mm) signal abnormalities/cystic changes, moderate-severe diffuse excessive high signal intensity (affecting several regions including subcortical white matter), or a 2 to 4 weeks’ delay in gyral maturation were defined as having moderate abnormalities. Infants were defined as having severe abnormalities if they exhibited parenchymal hemorrhage/periventricular venous infract, bilateral cystic periventricular leukomalacia, severe hydrocephalus/ventriculomegaly, or a greater than 4-week delay in gyral maturation on their term-equivalent age MRI., DTI data were transferred to an offline workstation for further image processing and analysis. We pre-processed all images using FSL 5.0 software of FMRIB Software Library (Analysis Group, FMRIB, Oxford, UK) and DTIStudio 3.0.2 of MRI Studio (Johns Hopkins University, Baltimore, MD). Briefly, we converted raw DTI DICOM data into analyze format using DTI Studio and imported this into FSL to perform eddy current correction. To further minimize the effects of motion and artifacts, we performed Automatic Image Registration (AIR) and automatic outlier slice rejection in DTI Studio. Next, we performed, tensor estimation and generated scalar maps (FA, MD, radial diffusivity [RD], and axial diffusivity [AD; L1 – lamda1]). Figure  illustrates examples of FA color maps at each of the four postmenstrual age time points. Last, in FSL, we employed the Brain Extraction Tool to perform brain extraction and BEDPOSTX (Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques) to run probabilistic tractography and model for crossing fibers. BEDPOSTX creates all the files for running probabilistic tractography by employing Markov Chain Monte Carlo sampling to build up distributions on diffusion parameters and model crossing fibers within each voxel of the brain. This software permits inclusion of datasets with up to 60 diffusion directions.Figure 5, Using the “ROI Tool” in Analyze 12.0 software (Mayo Clinic), the CC bundle was segmented on the most clearly delineated midbrain slice in the sagittal orientation. The “Auto-Tra […]

Pipeline specifications

Software tools FSL, MRI Studio, BET