Defining VOIs for Seeding and Imposing Restrictions

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Defining VOIs for Seeding and Imposing Restrictions

When arriving at the VOIs sub-page a fusion image is shown to the left which is composed of the Tensor image and the FA (Fractional Anisotropy) map. Note the two panels A and B in the upper right which correspond to these images, and the slider for mixing the respective contributions in the fusion image.

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In the lower right, the A and B images can be redefined. The mean diffusivity (MD), the DTI tensor as well as a masked version of the FA image are available for selection.

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VOI Definition

In PGEM, tractography is based on VOIs which can play different roles:

SEED VOIs: Tractography is started from the pixels in seed VOIs, following the local vector directions.

END VOIs: Only tracks ending in this VOI will be used. To avoid excessive pruning of tracks, an END VOI should have sufficient volume.

WAY VOIs: Only tracks passing through the WAY VOI will be used.

EXCLUDE VOIs: Tracks passing through an EXCLUDE VOI will be removed.

NEUTRAL VOIs: Such VOIs have no impact on tractography. Setting VOIs to NEUTRAL allows assessing the effect of END, WAY and EXCLUDE VOIs without the need of removing them.

TARGET: Is representing a VOI the track should end with.

VOIs can be created with the usual PMOD VOI tools. When creating a new VOI, a dialog window pops up which requires defining the appropriate Tracking property. Later on, this property can be changed using the VOI properties functionality as illustrated below.  

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In the following sections two VOIs will be used: a SEED VOI in the left corpus callosum created using the paint tool, and an elliptic VOI which will be used as a WAY VOI. The illustration below shows the VOIs on top of the FA image.

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After the VOIs have been defined, please proceed with the Tracking button in the lower right.

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Note the check box Vorticity&Helicity. If it is checked, PGEM calculates parametric maps called Vorticity Amplitude and Absolute Helicity, respectively. Vorticity is a measure of rotation, whereas helicity relates to the knottedness in fluids.

Tensor Inspection

The loaded tensor data can be inspected with the QC button. It shows a window with the projection of the principal diffusion direction vectors together with a color-coded direction image. Red indicates diffusion along the x-axis (left-right), green diffusion along the y-axis (posterior-anterior), and blue diffusion along the z-axis (inferior-superior).

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