MATLAB DSC Walkthrough¶

This guide covers dynamic susceptibility contrast (DSC) perfusion analysis using the MATLAB interface.

Launching¶

Add the main ROCKETSHIP folder to your MATLAB path, then start the DSC interface in one of three ways:

Command	Effect
`rocketship`	Launch the main interface, from which DSC analysis can be selected
`run_dsc`	Add the required subfolders to the path, then launch DSC analysis
`dsc`	Launch DSC analysis directly, assuming the subfolders are already on the path

Image selection¶

Select the source DSC images. These must be in NIfTI format.

Noise handling¶

Noise is estimated from a region of the image containing only air, and is used to establish the noise level of the acquisition. The region may be selected automatically from a corner of the image, or supplied as a binary mask in NIfTI format.

Arterial input function¶

The input function may be defined in three ways.

Option	Source
User Selected AIF	A binary mask supplied as a NIfTI file
Import AIF	A curve stored in a MATLAB `.mat` file
Use AIF from Previous Run	The curve derived by the most recent run

Fitting function¶

Select the form fitted to the measured input function samples.

Option	Description
Biexponential	Two-exponential decay fitted to the whole curve
Biexponential local	Two-exponential decay fitted over a restricted interval
Gamma-Variate	Gamma variate function, the conventional choice for first-pass DSC
Raw Data	No fitting; the measured samples are used directly
Upslope copy biexponential linear adjustment	Biexponential with the upslope replaced by the measured samples and a linear adjustment applied
Upslope copy biexponential	Biexponential with the upslope replaced by the measured samples

The gamma variate function is the standard choice where recirculation must be excluded from the first pass. Fitting reduces noise in the input function at the cost of imposing a fixed shape; the raw option preserves the measurement unmodified.

Input parameters and deconvolution¶

Specify the acquisition parameters, the tissue parameters, and the deconvolution algorithm used to recover the residue function from the tissue and arterial curves.

Bolus injection time¶

Option	Behavior
Automatic	Bolus arrival is detected from the signal intensity curves
User Selected	Bolus arrival is identified interactively

Bolus arrival timing determines which frames form the pre-contrast baseline, and therefore affects every derived quantity. Where automatic detection is used, confirm the result before interpreting the output.