3D Brain Atlas Tool | VivoQuant User Manual

Overview

The 3D Brain Atlas Analysis Tool is designed for automatic segmentation of brain image data. Automated fusion routines register an application-specific brain atlas to pre-clinical image data (or vice versa) and advanced statistical analysis methods are employed to provide rapid and thorough region-specific volume and uptake quantification.

Use the 3D Brain Atlas Tool to perform brain region analysis. The tool can handle CT or MR data as the input and MR, PET, or SPECT for the input functional data.

Warning: Please use caution when scaling data in this tool, as this can lead to errors in quantitation. For more information, refer to the Treatment of Quantitative Data page.

Install atlas

Please download and install the available atlases by going to Advanced Modules > Install Atlas > Mouse & Rat.

To change where the atlases are automatically stored, set via Advanced Modules > Install Atlas > Change Atlas directory option.

Typically the default path is located next to the VivoQuant cache:

Platform	Default path
macOS	~/Library/VivoQuant/atlas
Ubuntu	~/.VivoQuant/atlas
Windows	%appdata%/Perceptive/VivoQuant/atlas

For information on creating an atlas please refer to the How to create a Custom Brain Atlas page.

Prepare Image Data

Please load an anatomical image (CT or MR) and, if applicable, its corresponding NM data set before proceeding.

The tool requires the anatomical image from the data set to be loaded in the reference position. Any subsequent input images must be co-registered to the reference image prior to using the tool.

Providing a seed point is necessary if the images are not focused around the head/brain. To provide a seed point please place the cursor in the center of the brain in the Sagittal, Coronal, and Transverse views as seen in the image below.

Prepare MR Image Data

When using an MR data set as the reference image, a more accurate registration of the atlas can be achieved by performing an additional pre-processing step. Skull stripping the MR can be done semi-automatically using the 3D ROI Tool.

Segment Brain ROI

The ‘Spline Tool’ tab in the 3D ROI tool has an automatic thresholding tool which will allow the user to automatically segment the brain by providing a seed point on each brain slice. If necessary, the user can adjust the threshold for each individual slice to edit the automatic segmentation. To apply the segmentation for a given slice, use the green check mark button. To apply the segmentation and move on to the next slice, use the green check mark button with the red plus sign.

Cut Background ROI

Once satisfied with the brain segmentation on each slice, the user should cut the background ROI to complete the skull stripping. To cut the background ROI, set the background ROI as the output ROI and click on the ‘Cut ROI’ icon (circled in red in the image below) under the ‘Navigation’ tab in the 3D ROI Tool.

Result

All voxels that were not in the segmented brain ROI will be cut out of the image.

3D Brain Atlas Tool Settings GUI: Basic Settings

Getting There

To open the Atlas Tool settings GUI, please go to Advanced Modules > 3D Brain Atlas Tool

Basic Settings Tab

Data

Reference

Choose the reference image to perform the brain atlas

Registration Point

Select the registration point.

Choose “Head Center”: will center the reference’s head and do all the operations to present the brain atlas, it is the best method for cropped output. Options ‘Registration Direction’ and ‘Crop’ are enabled for this technique.
Choose “Cursor Seed Point”: will seed the operation with the crosshair point in order to present the brain atlas, it is the best method for non-cropped output. In this technique ‘Registration Direction’ is “Atlas to Data” and ‘Crop’ is unchecked, both always fixed.

Registration Direction

Select the registration direction.

Choose “Data to atlas” to transform the image data (including anisotropic scaling and shearing) to match the atlas.
Choose “Atlas to data” to transform the atlas to match the anatomical reference image.

Crop

Check the crop box if the data are not focused. The current head center (or seed point) will be displayed. To update the head center with the tool window open, use the mouse scroll wheel to move the crosshairs.

Atlas

Modality

Select the modality of the anatomical reference image. We currently support CT and MR images. If the image is tagged with modality information, the tool should detect this automatically.

Animal

Select the appropriate animal type.

For CT registration, we currently support mouse, rat, squirrel monkey, and cynomolgus monkey.
For MR registration, we currently support mouse, rat, canine, cynomolgus monkey, and rhesus monkey.

Atlas

Select the appropriate atlas type. These are populated based on the modality, animal type, and contents of the user’s atlas directory.

For information on creating an atlas please refer to the How to create a Custom Brain Atlas page.

Output Directory

Select the output directory in which to store results. If there are existing results in this directory, they will be deleted when the tool is run. To load the existing results click the Load button. The following will be stored here:

File	Purpose
atlasFinal.rhma	The output brain ROI
atlasFinal-anatomical.mhd	Anatomical reference used for registration
data.csv	Uptake and concentration data for each brain region for each input frame
data-montage.png	QC image of ROI fitted to data
settings.txt	Settings used to generate output
tmp-XXX.mhd	Output scans after transforms, starting with XXX = 000
tmp-XXX.raw	Raw file of associated with the pairing mhd file

Run the Tool

Click the Run button to begin processing. The dialog window will switch to the “Log” tab where progress updates are displayed.

Click the Cancel button to attempt to abort processing. This will stop processing after the current stage of processing has finished. As registration accounts for most of the processing time, this may not be responsive.
When the tool finishes, results will load automatically (including the CSV file) and VQ will finish in the 3D ROI tool.
Processing time will depend upon the computer’s inherent capabilities and the file size of the image files.

3D Brain Atlas Tool Settings GUI: Advanced Settings

Advanced Settings Tab

The advanced settings tab allows settings to be controlled that normally will not need to be modified.

Import 3D ROI

Check this box to use the ROIs currently in the 3D ROI tool instead of a specific brain atlas. If this box is checked, no cropping registration will be performed, and a new output spreadsheet will be generated. This is typically enabled (checked) when the tool has already been run before and ROIs have already been fitted and need to be adjusted, or when a .rmha file is provided to you by the analysis lead and you are required to manually fit the ROIs.

Atlas Key

The atlas key controls how the original atlas regions are mapped to the final atlas.

AllRegions (default): Combines left/right regions.
AllRegionsLeft: Retains left regions only.
AllRegionsRight: Retains right regions only.
AllRegionsLeftRight: Retains left and right regions.

Normalize to Region

Select an ROI from the drop down menu to normalize concentrations in the spreadsheet to that region.

Left/Right Split

Check this box to output both the original atlas and the split atlas. This only works if there are “Left” and “Right” keys for the selected atlas key. For example, “AllRegions” will work if “AllRegionsLeft” and “AllRegionsRight” exist.

Voxel Size

Change the voxel size of the output data if a different resolution from the input data is desired.

Lower values (higher resolution) are more computationally expensive.
Higher values (lower resolution) will speed processing but may reduce atlas ROIs to be unreasonably small.
Defaults to use same size as the starting image

Transform

Change the transform to restrict the number of transform parameters.

Versor: Rigid body transform, translation and rotation only.
Versor-Scale: Rigid body transform followed by scaling of the atlas (regardless of the registration option from basic settings tab).
Versor-Affine: Affine transform followed by minor scaling/shearing.
Affine: Affine transform only (faster but less robust than Versor-Affine).

Deformable Transform

Only for MR modality, the user can choose a deformable transform to use. Unlike rigid or affine transformations, a deformable transformation allows for the individual parts of the brain to be moved and warped independently.

None: no deformable transform is applied.
LogDemons: essentially a local displacement vector that moves a point in the moving image closer to a corresponding point in the fixed image, the update is then smoothed to ensure a smooth deformation.
SyN: Symmetric Normalization is a highly popular and effective deformable registration algorithm, its defining feature is its symmetric nature.

Quality

Change the quality to improve registration results and/or processing speed.

Fast: faster than standard, but less robust.
Standard (default).
Fine: slower than standard, but more robust (e.g. ideal for large rotations).

Save to iPACS

Check this box to upload images and ROIs directly to an iPACS.

Only iPACS servers that have been previously connected to via open DICOM will be listed.
Results will also be saved locally in the “Output Directory”.

Verbosity level

Change the level from 0 to 3, higher the value the higher the level of verbosity.

Manual Correction

Sometimes automatic registration will be poor and will need manual correction.

To manually edit the registration, load the ‘atlasFinal-anatomical.mhd’ file from the output directory and place it in the reference position. Navigate to the Reorientation/Registration operator and manually correct the registration:

Data to Atlas (seen in example image below): Register all inputs to the atlas anatomical reference.
Atlas to Data: Register the atlas anatomical reference to the input anatomical. Apply this transform to the ROI.

Once satisfied with the registration, unload the atlas anatomical reference and rerun the tool using the “Import 3D ROI” option under the advanced settings tab.

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