24. Dynamic Analysis¶
24.1. Dynamic Analysis Commands¶
The Dynamic Analysis tab contains commands for processing dynamic (four-dimensional, 4D) data. These commands are broken down into two types.
1. Commands related to model analysis. These include tools for processing dynamic contrast-enhanced MRI, PET, and CT, diffusion-weighted MRI, intravoxel incoherent motion (IVIM) MRI, T1 and T2 mapping, and other acquisitions. These commands open dialog panels with multiple user-defined options and are described in separate sections:
2. Commands for manipulating dynamic datasets or one-step quantification. These commands are divided into several groups that are described below:
24.2. Preparing 4D Data for Analysis¶
Dynamic datasets usually consist of series of 3D volumes acquired at different values of a dynamic variable, such as time, b-value, echo time (TE), inversion time (TI), flip angle (FA), etc. Dynamic data in DICOM format can be loaded into FireVoxel using File > Open DICOM commands.
As a rule, FireVoxel automatically determines the type of dynamic data and reads the dynamic variable from the DICOM header. After loading images into FireVoxel, the user should check if the dynamic variable has been read correctly. For each 3D volume, the corresponding value of dynamic variable is displayed in the lower left corner of the main software window. The user can switch between images with different dynamic variable (e.g., time points) using Right and Left keys on the keyboard (in both the Slice view and the Film view). To scroll through slices of a 3D image, the user can use the mouse wheel or Up and Down arrows on the keyboard.
Once the 4D images are properly loaded, they can be pre-processed (for example, co-registered and/or segmented, if necessary) and then analyzed using various processing methods to determine tissue parameters.
24.3. Aggregate (group)¶
24.3.2. Aggregation Residual¶
24.3.3. Aggregation Relative Residual¶
24.3.4. Aggregate by Median selection¶
24.4. Dynamic (group)¶
These commands require the dynamic image to be the active layer. If the active layer is not a 4D image, an error message is shown: 4D volume is required. The Dynamic commands open a dialog (Specify time interval) that prompts the user to enter the index of the first and last points (labeled T0 index and T1 index, respectively) of the interval of dynamic variable to be analyzed.
By default, then entire range of dynamic variable is included between the first time point with T0 index = 0 and the last point with T1 index = N-1 (where N is the total number of dynamic points).
The Dynamic group commands determine signal maximum (Max), integral, or average within the [T0, T1] interval and return the results as 3D voxel maps placed in new, automatically created layers. These new layers are named the same way as the original image.
24.4.1. Dynamic Max¶
Create a map with each voxel containing maximum signal intensity in that voxel over the user-specified interval of time point indices. The result is an integer 3D image.
24.4.2. Dynamic Integral¶
Create a map with each voxel containing the integral of the signal intensity in that voxel over the user-specified interval of dynamic variable. The result is a real 3D image.
24.4.3. Dynamic Averaging¶
Create a voxel map with each each voxel containing the average signal in that voxel over the user-specified interval. The result is a real 3D image.
24.5. Gradient and Mutual Info (group)¶
24.5.1. Image Gradient Average over Time¶
24.5.2. Basic 4D Gradient¶
Requires a 4D image. Creates a 3D image with width, height, and number of slices the same as in the original image, in which each voxel contains the signal gradient. ADD DETAILS
24.5.3. Calculate Cross4D Mutual Info over ROI¶
Requires a 4D image and a visible ROI layer. Returns the value of Cross4D mutual information in the image processing dialog (Cross4D Mutual Info over ROI [value]). Use Ctrl+C Ctrl+V to copy and paste the dialog information elsewhere.
If there is no visible ROI layer, an error message is shown (ROI is required in this operation). If there are two or more visible ROI layers, but the active layer is an ROI layer, the command will be executed using this layer. If there are two or more visible ROI layers, but none is the active layer, an error message is shown (Ambiguous layer configuration). The user must select one ROI layer as the active layer, or uncheck the visibility boxes for all ROI layers but one, for which the command will be executed.
24.5.4. Calculate Cross4D Mutual Info Norm over ROI¶
Requires a 4D image and a visible ROI layer. Returns the value of Cross4D mutual information norm in the image processing dialog (Cross4D Mutual Info over ROI [value]). Use Ctrl+C Ctrl+V to copy and paste the dialog information elsewhere.
If there is no visible ROI layer, an error message is shown (ROI is required in this operation).
If there are two or more visible ROI layers, but the active layer is an ROI layer, the command will be executed using this layer.
If there are two or more visible ROI layers, but none of them is the active layer, an error message is shown (Ambiguous layer configuration). The user must select one ROI layer as the active layer, or uncheck the visibility boxes for all ROI layers but one, for which the command will be executed.
24.6. [Manipulate] (group)¶
24.6.1. Extrapolate Multi-echo volume into TE=0¶
Requires a 4D MRI dataset acquired with echo time (TE) as the dynamic dimension. Opens dialog (Volume Smooth parameters) with extrapolation parameters (Fig. 24.1).
VERIFY Next, opens dialog (Specify Air threshold) to enter the signal intensity threshold value below which voxel intensities will not be processed and will be instead replaced with zeros.
Creates a 3D volume calculated by extrapolating data, voxel by voxel, to TE=0 ms.
If the dynamic dimension is NOT the echo time, shows an error message (Echo Time dynamic dimension is expected).
Note: FireVoxel determines the dynamic dimension automatically when images are loaded. If your 4D data are opened in FireVoxel with a wrong dynamic dimension, check the loading step first and if this does not solve your problem, contact the FireVoxel team.
24.6.2. Remove all Dynamic Dimensions except Time¶
ADD CONTENT Requires a 4D dataset. Removes dynamic dimensions except time.
24.6.3. 4D Volume to Principal Components (PCA)¶
VERIFY Requires a 4D dataset (dimensions WxHxDxN). Opens dialog (Specify Integer) to enter the number of principal components to keep (P). By default, the number of principal components is the same as the maximum length of the fourth (dynamic) dimension (N).
Creates a new document (titled [original]_PCA) with the principal component analysis of the original 4D image and dimensions WxHxDxP.
24.6.4. Convert 3D layers to 4D volume¶
VERIFY Requires a 3D volume.
24.6.5. Dynamic Dimension support¶