Computational protocol: Lesion Location-Based Prediction of Visual Field Improvement after Cerebral Infarction

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Protocol publication

[…] Patients underwent 1.5-T MRI scanning (Siemens Avanto, Siemens Medical Solutions). DWIs were obtained by a single-shot spin-echo echo-planar imaging technique with repetition time of 3000 ms, echo time of 86 ms, 0.651 × 0.651 × 5 mm3 resolution with 2 mm gap, 384 × 384 in-plane voxels. Additionally, patients underwent 3-T MRI scanning (Philips Achieva; Philips Medical Systems) at 1 week after symptom onset to obtain high-resolution T1-weighted MR images (MP-RAGE, voxel size = 1 × 1 × 1 mm3).An ischemic lesion mask was extracted using FSLView toolbox in FMRIB Software Library (FSL) in its native DWI space []. The ischemic lesion was delineated by manual drawing of the margin of the DWI lesion by an investigator (Y.-H.K) under supervision by a stroke neurologist (D.-W.K) who were blind to any clinical information. The lesion volume was calculated in its native space.Registration of the lesion mask from its native space to a standard Montreal Neurological Institute (MNI) space was performed via the FMRIB Linear or Non-linear Image Registration Tool implemented in FSL (FLIRT or FNIRT, respectively). In detail, co-registration was performed to estimate the rigid body transformation parameter between an individual apparent diffusion coefficient scan and a high-resolution individual T1 scan via FLIRT with normalized mutual information cost function. Spatial normalization was performed to estimate affine transformation and local deformation parameters between a high-resolution T1 scan and the standard MNI T1 scan via FLIRT and FNIRT with excluding lesion mask option in the non-linear registration stage. The lesion mask in diffusion space was transformed into standard MNI space by applying the rigid body transformation, affine transformation and local deformation parameters. The rEIL in each individual cortex was calculated on the automated anatomical labeling (AAL) atlas in the standard MNI space [] to quantitatively calculate the regional damage as follows: (the volume of lesion inside the individual gyrus / the total volume of individual gyrus)×100 (%) (). […]

Pipeline specifications

Software tools FSL, AAL
Application Magnetic resonance imaging
Organisms Homo sapiens
Diseases Cerebral Infarction, Brain Ischemia, Stroke, Infarction, Posterior Cerebral Artery