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A. Introduction

The Slice MRI Motion Estimation and Reconstruction (SLIMMER) tool is intended to allow the formation of a single 3D high resolution image from multiple sets of lower resolution multi-slice MRI data, where regional tissue motion can occur between the acquisition of slices. The input data is a set of raw DICOM format multi-slice data. The final output is a single volume image in GIPL or NIFTI format. The plugin tool for rview provides a graphical user interface to load data, automatically initialize the stack alignment from scanner coordinates, select the region of interest and then to inspect the result of regional between-slice motion estimation, bias inconsistency correction and volume reconstruction algorithms.

The SLIMMER tool loads raw DICOM files, performs motion correction and builds a 3D reconstructed volume. SLIMMER tool forms stacks from raw DICOM images of 2D slice, and assists to align them to the reference space. It performs slice-stack and between-slice motion correction of user selected anatomical regions appearing in multiple multi-slice imaging studies and builds a full 3D volume from the motion scattered slice imaging data. It provides a graphic user interface to apply algorithms for the Slice Intersection Motion Correction (SIMC) [1][4], slice bias consistency correction [2][5] and 3D volume reconstruction [1][3].

This manual focuses on how to use the SLIMMER tool to load data, how to apply stack and slice motion correction, and how to reconstruct the final 3D image. A general manual for RView can be accessed from the RView menu, by selecting RView-Help...Manual Contents. (You need an internet connection.)


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