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[edit] AnatInit

anatInit is a GUI for initializing anatomical images. It is part of the mrVista2 toolbox. It covers the following steps:

  • Converting individual anatomy images from raw DICOM/I-files to Analyze format
  • Aligning and averaging multiple Anatomical images
  • Iso-voxeling (resampling at 1mm)
  • Selecting the points for rotating the anatomy into AC/PC space
  • Saving ANALYZE (or compressed NIFTI) and vAnatomy.dat files

It is essentially a shell for the mrAnat tools described in Anatomical_Methods.

[edit] Usage

To use anatInit, first make sure you have the mrVista 2 tools in your path. Ensure the toolbox is downloaded, cd to the root directory (mrVista2/) and enter:

> mrv2Paths

Now cd to the directory containing the anatomies you want to initialize. In this case, let's assume you have three directories containing DICOM files, in the directories Raw/001, Raw/002, and Raw/003:

> rawFiles = {'Raw/001' 'Raw/002' 'Raw/003'};
> anatInit(rawFiles);

The code will first convert the data in each Raw directory into a temporary ANALYZE format file called 'tmpAnatInit1.img', 'tmpAnatInit2.img', and so on. It will then open up a mrViewer UI for the first ANALYZE file, as well the anatInit GUI.

The mrViewer UI is there in case you would like to select the three points (AC, PC, and mid-sag) for aligning the final volume into AC/PC space. This is not necessary, so if you were to set the output file and press "GO" on the anatInit GUI, it would align, average and isovoxel the anatomies without rotating into AC/PC space.

If you'd like to select the points using the viewer, here's how:

  • Use the navigation panel to page between slices.
  • To facilitate locating yourself in the anatomy, it's recommended you select "3-Axis View" in the Navigation Panel. Also, under the "Coordinates" menu in the main window (title bar "tmpAnatInit1"), select "I|P|R". This will rotate the displayed images into an iso-voxeled coordinate space, in which (rows, cols, slices) are increasingly (Inferior, Posterior, Right). In other words, the three orientations will be Sagittal, Coronal, and Axial slices.
  • Find the anterior commissure (described in the Talairach section ). Select "Set AC" in the anatInit GUI. (The GUI will convert back to ANALYZE pixels for you, so the value set there may not match the cursor position in the viewer)
  • Find the posterior commissure. Select "Set PC" in the anatInit GUI.
  • Find a point along the mid-sagittal line, in the same coronal slice as the AC. Select "Set Mid-Sag".
  • You're good to go. Now the resulting volume will be rotated as well as iso-voxeled.

To save the output file as NIFTI instead of ANALYZE, set the extension on the output file (in the anatInit GUI) to ".nii" instead of ".img".


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