Create a custom Brain Atlas | VivoQuant User Manual

How to create a Custom Brain Atlas

A custom brain atlas can allow the user to perform other registrations based on your own ROIs, and on images of other animal species. This can be done with the provided wizard in VivoQuant.

The following files comprise an atlas:

Item	Format	Description
Reference image	.raw	The reference image data on which your ROI atlas has been segmented
Reference Image Header	.mhd	The header corresponding to the raw reference image
ROI Atlas	.rmha	The segmented regions of your reference image in which you’d like to use as an atlas
ROI Key	.csv	A CSV file of the region names in the order that they appear in the rmha file

Note: These files will be located in the configured atlas path.

Note: The tool can handle CT or MR data as the input and MR, PET, or SPECT for the input functional data.

Creating a custom atlas with the wizard

Open your data then go to the 3D ROI Tool. Load in the ROI(s) (stored either locally or on iPACS):

Load ROI
The ROI(s) should be available in the ROI selector and should also appear on the ROI table:

Loaded ROI
Navigate to Advanced Modules > 3D Brain Atlas tool, then select the + button:

Brain Atlas Tool menu

Add new atlas
Follow the steps prompted by the Brain Atlas Tool Wizard to select reference images and ROIs.

Selected loaded ROIs

Selected loaded ROIs

Set atlas name

Important: When choosing the animal name, ensure that there is a corresponding entry in the specieslist.txt file, or the atlas will not appear 3D Brain Atlas Tool dialog.

Add key files

Important: If selecting manually generated keyfiles, at least two must be selected in the file dialog (one left and one right) with CTRL+select (as appropriate for your platform). The filenames must match the either atlasName-Left.csv or atlasName-Right.csv

Saved documents

Saved output

The custom atlas should be ready to use.

The specieslist.txt file

If you should need to create an atlas for another species, you can do so by editing the specieslist.txt file that’s located next to the VivoQuant application. Typically, this file can be found at the following locations:

Windows: C:\Program Files\inviCRO\VivoQuant\specieslist.txt

macOS: /Applications/VivoQuant/Contents/MacOS/specieslist.txt

Important: On some platforms, you may need administrator access to modify this file.

Tip: Users can make variations on species’ names if an atlas is needed on a specific data type. For example, a PlanarMouse and VolumetricMouse species name could be created.

Key file format

Content

The key file is a comma separated text file without a header row. Empty lines, or lines starting with # or $ are ignored.

The line format is:

input index of the ROI in the .rmha file,output ROI index in the resulting segmentation,ROI name

For example, the keyfile below corresponds to an .rmha ROI file which has 28 disjointed ROIs, which will map to 14 regions in the resulting output segmentation:

Filename

The wizard will generate a key file with the following name format:

atlasName-Key-nRegionsRegionsdirection.csv

The atlasName is entered by the user in the wizard process.

The nRegions value will be either All if all ROIs in the current layer were selected to be used, or the number of ROIs.

The direction value could be one of Left, Right or LeftRight if the user has ROIs with the text left or right (case insensitive) in the ROI names. It will be empty if none of the selected ROIs were named this way.

This pattern could be used to create segmentations for left cerebellum and right cerebellum separately, or cerebellum combined.