![]() You can now: 1) quit by pressing q in which case the result is then piped to the vmtkimagewriter instance, or 2) go on by pressing i once again and defining another VOI. Normal interaction with the image planes is still active, so you can still move them as explained before.Īt this point the image volume will be clipped with the region selection cube (widget) and the new volume will be displayed in the render window.Resize the cube by left-clicking and dragging the little spheres (handles) on the faces of the cube.Translate the cube by middle-clicking on it.A yellowish cube will then appear which will be the tool used to select the VOI. When the render window pops up, pressing i will activate the interactor. (this time I chose to use the built_in writer in vmtkimagevoiselector instead of piping to a vmtkimagewriter. Vmtkimagevoiselector -ofile image_volume_voi.vti Vmtkimagereader -f dicom -d dicom_directory_path -pipe To extract a volume of interest (VOI) from a dataset, one can pipe an instance of vmtkimagevoiselector between the DICOM reader and the writer in this way: Often, medical images contain structures which are not of interest. Meshes: vtu (VTK XML), xml (Dolfin), xda (libMesh), msh (Fluent), fdneut (FIDAP), lifev (LifeV), tec (Tecplot).Surfaces: vtp (VTK XML), stl (Stereolithography), tec (Tecplot). ![]() Images: vti (VTK XML), mha (Meta Image), nrrd (NRRD).No processing should be carried out on them since important information and details can be lost by rescaling levels.) File formats (Use of 8-bit images should be limited to display purposes only such as those used in presentations or publications. ![]() You can adjust that with the -windowlevel option of vmtkimagewriter. For 8-bit formats, image levels will be automatically scaled to 0-255. If the image volume is composed by more than one slice, single slices will be output in separate png files named image_file_prefix0001.png, image_file_prefix0002.png, image_file_prefix0003.png, etc. ![]() ![]() Vmtkimagereader -f dicom -d dicom_directory_path -pipe vmtkimagewriter -f png -ofile image_file_prefix ![]()
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