Brain Follow-Up - Introduction

The Brain Follow-Up tool is used to detect focal changes in brain images that occur over time. The tool works with images collected at two or more time-points, and with one or more image contrasts. The images with one particular contrast (chosen by the user) are co-registered to a common template. This template can be constructed iteratively from the average of the images at the different time points, and will be at a position that is the geometric average position of the input images. The registered images are then intensity rescaled, and any intensity bias caused by non-uniform reception properties of the MRI receiver coils is corrected, before a subtraction is performed to show the differences between the images at the different time points.

The input images must:

  1. Have an axial orientation.
  2. Cover the brain only, without excessive neck within the range of slices.
If the images are not in an axial orientation, you can use the Image Resampler or Multi-Planar Reconstruction to re-orient them to axial. If the image slices extend into the neck, you can crop the images using either the Image Resampler or Multi-Planar Reconstruction.

Start the Brain Follow-Up tool from the Toolkits menu: Launching the Brain Follow-Up tool
This will bring up:

The Brain Follow-Up tool

Input Images

You set the number of time points to be analysed using the Spinner to set the number of time points to be analysed spinner, and the number of image contrasts using the Spinner to set the number of image contrasts to be analysed spinner.

This will alter the size of the N Time-Points × M Contrasts matrix of image selection panels below. For each image selection panel in the matrix, you must select the appropriate input image corresponding to the time point and contrast for that column and row.
Note: only the first image contrast (set in the top row of the matrix) will be used for spatial registration. The other image contrasts will simply be transformed using the same transformation as was found for the first contrast. The images with the other image contrasts must therefore already be in register with the first contrast at the corresponding time-point. If necessary, they can be registered to the first contrast image using the Image Registration tool.

After the analysis is complete, Jim can automatically present images for review. If you want to take advantage of this, select which image contrast you want to review using the Radio button for selecting which image contrast you want to review radio button at the end of the row for that contrast. You can only review one of the image contrasts. Then select which pair of time points you want to review using the Radio button for selecting which pair of time points you want to review check boxes below the columns for those time points. You can only review one pair of time points.

You can now go on to setup the other options for analysis.

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