MorphoDig tutorial 14: mask regions of µCT data

MorphoDig tutorial 14: mask regions of µCT data


Drag and drop the project (.NTW) file inside the main 3D window. You may hide the grid. Then open the “edit first selected volume” window Click on “Enable Mask” Masking tools become available Let’s use the “Pencile sphere” tool, and set pencil radius to 100 (screen) px “T” + left click=>activates pencil tag tool.
“T” + mouse roll=> increases /decreases pencil radius Here we have used ” pencil sphere” + “mask inside” Click on “invert mask” . Previously visible regions are now masked, and what was masked is now visible Click on “Pencil tube”. Then press “T” + left click. The newly masked region has a cylindric shape Let’s use the “mask outside” option “T” + left click (pencil tube + mask outside options)=>what remains visible is tubular. Let’s play with the “shift” slider to visualize all unmasked bones. Masks can be reitinialized. Now use the lasso to mask all bones except the cranium and the mandible. Click on “Export mask”=>then export the mask as a metaimage MHD/MHA file Masks MHD/MHA can be read with Fiji. They are 8 bits volume. All masked regions are “black” (0) and all visible regions are “white” (255). Let’s use the “Mask using first selected surface” option. Let’s create an icosahedron with a 15 mm radius. Move this sphere at the desired position (CTRL + middle click drag) Click on “Mask using first selected surface” button (Mask Inside option activated) All voxels inside the sphere are now hidden. Mask reinitialization Now activate the “Mask outside” option. Click again on “Mask using first selected surface” button. Only voxels situated within the sphere remain visible. Previously exported masks can be reimported. Click on “import mask”. Choose the previously exported mask Click on “harden mask” This option will modify the original µCT data and will replace all masked voxels with “0”. Note that volume name was postfixed with “_hrd” Let’s saved the modified volume Open the newly created Metaimage (MHD/MHA) file with Fiji. Note that all the postcranial bones that had been masked are now removed from theses data.

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