QSM Input Requirements

Input Images

The input image(s) must be complex (real/imaginary or magnitude/phase) images acquired at different echo times (TEs). The complex components may be contained in separate image slices, or the image may of data type Complex, with interleaved real and imaginary components. Jim is able to automatically detect the type of input image that you have. In case of difficulty, contact E-mail address for support.

There may be a single input image containing all image slices for all TEs, or there may be multiple input images (one for each TE). In the input configuration section, select the type of input image(s) you have:

Input images for Quantitative Susceptibility Mapping

Select:

  • A single input image for Quantitative Susceptibility Mapping for a single input image containing all slices for for the first echo, followed by all slices for the second echo etc. The image can be either 3-D or 4-D, where the fourth dimension is the echo time.

  • Multiple input images for Quantitative Susceptibility Mapping if there is one input image per TE. The input configuration section then changes to look like this:

The Quantitative Susceptibility Mapping tool

Select the images by pressing the Button to select the input images for ASM button. Use the Button to move an image up the list and Button to move an image down the list buttons to reorder the images in order of increasing echo time.

If you have multiple input images, all must have the same dimensions (matching numbers of samples in the row/column/slice directions).

Interior Mask

In Quantitative Susceptibility Mapping, defining an interior region is necessary to exclude boundary areas where severe magnetic field distortions occur; this helps prevent artifacts from corrupting the tissue susceptibility calculation. You can define the interior region in one of two ways:

Selection to use an image mask to define the interior region. An image mask consists of an image with the same number of rows/columns/slices of pixels as the input image(s). In the mask image, pixels which are non-zero intensity are in the interior region and pixels with zero intensity are in the exterior region. Set the mask image using the panel below:

Panel for selecting an image mask

Selection to use a ROIs to define the interior region. You can use a set of ROIs as a mask. Pixels that are inside any of the ROIs are in the interior region and pixels that are outside all the ROIs are in the exterior region. Select the mask ROI file using the panel below:

Panel for selecting an ROI file mask

You may find the Brain Finder useful for creating the mask image or ROIs if you are working with head scans.

You can now go on to the first processing stage, which is phase unwrapping.