Getting starting with the VAI analysis

Data formats

The VAI module supports both Dicom and Nifti image formats. For Dicom images , the VAI perfusion series must be present as a single series containing the dynamic data for both echoes. Both the perfusion, and structural series must be multi-slice. Sorting of the 5D series is done automatically at VAI module startup. The sorting is performed according to the information detected in the Dicom header. For Nifti images data must also be loaded as a single series containing both echoes. If the GRE and SE series are stored as separate Nifti files, they can readily be merged into a single series by selecting the two files in Windows Explorer and dragging them into nordicICE. Note, that the GRE series then needs to be the first file selected in the drag&drop procedure. For Nifti data, the echo times and temporal resolution must be set prior to processing. This is done in the <Image format> tab.

Starting the VAI module

The module is started from the ‘Modules’ list in nordicICE main menu like other standard nordicICE modules.

The active datasets (the one selected) upon starting the VAI module should be a structural dataset – i.e. the dataset used to define volume of interest (typically pathological area lesion/edema etc). This should be a multi-slice structural dataset covering the anatomical region included in the perfusion data. In addition, a perfusion dataset should be loaded into the nordicICE workspace prior to launching the VAI module. This must be a multi-slice dynamic dataset, and can be either a single echo DSC-MRI or a double echo GRE-SE dataset.

Both Dicom and Nifti data formats are supported.

When launching the VAI module, the screen should look something like this:

Figure 1: Main layout of VAI module GUI

As shown in figure 1, the perfusion dataset, present in nordicICE workspace when launching the module should appear in the ‘Source datasets’ panel on the left-hand side of the MPR windows. This is then activated by drag&drop into panel 4 as shown in figure 2.

Figure 2: Selection of functional dataset by drag & drop into panel 4.

Note that multiple structural datasets can be present in the source dataset panel and any active data can be replaced by drag & drop of available datasets in the left source data panel. Currently, only one functional dataset can be activated by drag & drop. If a new functional series needs to be activated, the VAI module needs to be closed and re-opened and then drag in the new functional dataset. Figure 2 also shows the slide bars used to select slice / dynamic scan for the respective datasets. For the functional data, it is also possible to select which echo time (TE) data should be visualized, if double echo GRE/SE data was loaded.