Computational protocol: Diffusion tensor imaging in metachromatic leukodystrophy

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Protocol publication

[…] Diffusion tensor imaging data were analyzed using FMRIB’s software library FSL after correction of eddy current distortion and subject motion. The diffusion tensor was fitted resulting in maps of FA, AD, RD and MD. Tract-based spatial statistics (TBSS) was used to align FA images from all subjects into a common space and to create a mean FA skeleton. The aligned FA images of all participants were projected onto this skeleton and fed into voxel-wise crossparticipant statistics using randomise (see “”) [].Based on the regional differences found in the TBSS analyses, we further analyzed diffusion measures in the following regions of interest (ROIs): normal-appearing white matter (NAWM, corpus callosum and thalamus in all subjects, and abnormal cerebral WM in patients. In addition, we analyzed the pyramidal tracts, which were determined for each subject by tractography between motor cortex and cerebral peduncles (see below).To determine these ROIs in DTI subject space, we first outlined abnormal WM on 2D FLAIR images of patients using clusterize, a semiautomatic segmentation algorithm involving iterative region growing followed by interactive selection of abnormal WM clusters []. The mask of abnormal WM was registered to the corresponding 3DT1, and filled with signal intensity resembling NAWM []. This 3DT1 image was then segmented with the FSL tools FAST [] and FIRST [] to obtain WM, gray matter (GM) and deep GM (DGM) structures, including the thalamus. DGM and abnormal WM were subtracted from the WM mask to obtain NAWM. ROIs for corpus callosum and cerebral peduncles were identified using the Johns Hopkins University (JHU) WM atlas defined in standard Montreal Neurological Institute (MNI) space []. The motor cortex was identified in MNI space using the Automated Anatomical Labeling (AAL) atlas []. ROIs in MNI space were warped into 3DT1 subject space after linear and non-linear registration using FSL tools FLIRT and FNIRT. All ROIs were subsequently registered to DTI subject space using nearest neighbor interpolation.The ROIs of motor cortex and cerebral peduncles were used as seed and target for probabilistic tractography using the FSL tools bedpostx and probtrackx2 to obtain the left and right pyramidal tract []. Mean diffusion measures within the pyramidal tracts were determined by weighting the underlying FA and diffusivity maps by the probability of a voxel within the tract. […]

Pipeline specifications

Software tools AAL, Probtrackx
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens
Diseases Leukodystrophy, Metachromatic, Lymphoma, Non-Hodgkin