Publication Data from Koch et al 2017

Please ignore this version and check out the latest version of the record. Do not use the toolbox provided here. The latest version of the toolbox is available under

Contains the dataset and the MATLAB toolbox used for Koch et al. (2017) "Atlas registration for edema corrected MRI lesion volume in mouse stroke models"

T2 weighted MRI data in NIFTI format from stroke mice 24 h post surgery. Contains raw data (images before registration, manually delineated hemisphere and lesion masks) and processed data (automatically generated brain mask and an additional version of raw images in registration to the Allen mouse brain atlas). Also contains a copy of some datasets for which slices in the image stack were removed. Includes an excel file describing the group assignment of each mouse (middle cerebral artery occlusion, photothrombosis or sham, full number of slices or partial number of slices) and describing files for each mouse. Histological data (TTC stainings) and corresponding regions of interest in ImageJ format are stored in a separate folder.

Contains the MATLAB toolbox for registration of T2 weighted mouse MR images to the Allen brain atlas. Only included if a reproduction of results is needed. A more recent version of the toolbox is available under


Brief introduction for basic usage of the ANTX toolbox.




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