32. T2 and T2* Mapping

32.1. T2 or T2* data

Relaxation times T2 and T2* are usually determined from 4D MRI data acquired with multiple gradient echo sequences at different echo times (TE). These images are then analyzed with an appropriate model (e.g., monoexponential or bi-exponential) and fitted values of the relaxation times are determined as a result. The processing routine for T2 or T2* relaxometry is similar to the routine for DWI.

32.2. Compute T2 or T2*

  1. Load images. Use Open > Open DICOM folder: Single Document. This opens the DICOM Tree Dialog. Select the multiple gradient echo series and click Load. The images will be loaded and displayed in a new document window.

  2. Check images. Verify that the 4D images were loaded correctly by scrolling through the dynamic variable. Click the right arrow key on the keyboard several times. The image intensity must decrease as the echo time increases.

  3. Check dynamic variable. Now check that FireVoxel correctly read the dynamic variable, TE. Open the Layer Control and click Info. The layer information panel will open. Click on the lower right part that shows a summary of the main DICOM fields and scroll to the bottom. This part usually displays the dynamic variable for every frame of the 4D image. For T2 or T2* data, this part should show a list of echo times (in seconds). If this list is not displayed, check your data and/or contact the FireVoxel team for assistance. If you see the correct TE values, you proceed with your analysis.

  4. Segment the tissue or organ of interest. You can define these ROIs manually (see Drawing raster ROIs), or using a combination of manual drawing and ROI tools (see ROI> Morphology>Fill 2D Contours and Fill Convex), or with fully automatic tools (Segment 3D: EdgeWave). The segmentation mask will reside in an ROI layer. Label ROIs clearly if multiple ROI layers are present in the document.

  5. Perform model analysis. Make sure that the base layer is active and the ROI is visible. Select Dynamic Analysis > Calculate Parametric Map or click param_map toolbar icon.

    The Parametric Map Calculation dialog will open. In the Model dropdown menu, select Model 16. T2 or T2* mono-exponential mapping. In most cases, the default values of hyperparameters are acceptable. Select at least one output parameter (usually T2 or R2).

    Select the processing option by clicking one of the buttons at the bottom of the dialog: Process all, Process ROI only, Process volume as a single curve. Note that Process ROI only is available only when there is a single visible ROI in the document.

    When the user clicks a button that initiates voxel-by-voxel fitting, a summary dialog with the data, model, and ROI is shown, and the user is asked to confirm these details. Once the user clicks OK, processing starts and may be time consuming for large voxel maps.

    If the user selects Process ROI/volume as a single curve, there is no confirmation screen, but instead the results are returned in the Dynamic Experiment Single Curve Results dialog. This dialog shows the plot of data and model curve and a table of parameters, as well as controls for customizing this plot and generating report.

  6. Inspect modeling results. The results of voxel-based analysis are returned in automatically created real-valued layers and the maps are displayed as colormaps. Activate the parametric maps in Layer Control and select ROI Stats 3D to explore the parameter statistics.

  7. Save modeling results. The easiest way to save the parametric maps is to save them together with the data as a FireVoxel document (.fvx). Alternatively, these maps can be saved as NIfTI images. Activate the map in Layer Control and select Save as Image > (NIfTI) or select File > Save Active Layer as Image > (NIfTI).