QSM Standalone

How can we map the magnetic susceptibility sources from local field map?

A local field (or tissue field) is the field generated by the magnetic susceptibility sources from the brain tissue. The assumption of the field generated by a magnetic susceptibility point source is a dipole field. We can then try to compute the susceptibility values by deconvolving the local field with a dipole field. However, due to the fact that the dipole field in the k-space (i.e. the dipole kernel) has zero values on the cone surface at 54.7° and values close to this surface will also be close to zeros. As a result, the number of unknown parameters is more than the measurements we have in the data, leading to the problem ill-conditioned and the resulting QSM map has the so-called streaking artefact. To solve the ill-conditioned problem, most of the QSM algorithms try to add a regularisation term in the QMS dipole inversion problem, imposing spatial smoothness in the QSM map and/or the QSM map has similar anatomical features as shown in the magnitude images in order to reduce the streaking artefact in the QSM result.

Structure of the application

This standalone consists of two panels:

• I/O panel, and

• QSM panel.

Description of each panel is given below:

I/O panel

The I/O panel is responsible for data input/output and data processing that is not specific to QSM.

• Data input

  There are two pathways to specify input in this application:

  1. Specify a directory that contains all essential data.

  The essential data are:

  Data	Description
  Local field	3D local (tissue) field map ([x,y,slice]) in Hz, must contain ‘localfield’ in the filename, e.g. localfield.nii.gz
  Magnitude	(optional) 4D magnitude data ([x,y,slice,time]), must contain ‘mag’ in the filename, e.g. mag.nii.gz
  Weights	(optional) 3D weighting map ([x,y,slice,time]), must contain ‘weights’ in the filename, e.g. weights.nii.gz
  Header	see SEPIA header for more information, must contain ‘header’ in the filename, e.g. header.mat
  Mask	3D signal mask, if provided, must contain string ‘mask’ in the filename, e.g. mask.nii.gz

  Warning

  Please make sure the filenames follow the above rules (see also Data Input in Data Preparation) and no other files in the directory sharing the same string labels (i.e. ‘localfield’, ‘mag’, ‘weights’, ‘header’ and ‘mask’).

  2. Specify the required data separately using the GUI buttons.

  Note

  Depending on the QSM dipole inversion algorithm selected. The ‘Magntude and ‘Weights’ input are optional input.

• Output prefix

  By default, the output files generated by SEPIA will be stored in a directory named ‘output’ under the directory of the input files (i.e. ‘_/your/input/directory/output/_’). The prefix of the output filename is ‘Sepia’. You can change the default output directory and prefix according to your preference. If the output directory does not exist, the application will create the directory.

  Note

  Make sure the ‘Output prefix’ field contains a full path of the output directory and a filename prefix.

• Brain mask

  You can specify a signal (brain) mask NIfTI file.

  Note

  A mask must be provided (either in the input directory or specified) in this standalone.

QSM panel

• Method:

  Select a QSM dipole inversion method. The method parameters will be displayed on the method panel.

• Reference tissue

  Select a tissue for QSM value referencing.

  Warning

  The ‘CSF’ tissue option works only when multi-echo magnitude data is provided.

Others

• Load config

  Import the method related settings specified in the SEPIA-generated config file to the SEPIA GUI. NO modification will be made in the I/O panel.

• Start

  Generate a SEPIA config file that contains all user-defined methods and parameters for QSM processing based on the setting in the GUI. SEPIA will run the config file immediately once it is generated.