From Van Essen Lab

Jump to: navigation, search


Segmentation in Caret

The SureFit segmentation process starts with an anatomical volume and its end product is a surface model. It is important that the surfaces produced are topologically correct. This means that the surfaces must not contain any holes (sometimes called handles). Topologically correct surfaces are required for proper surface flattening and registration.

Special Note

The SureFit algorithm stores a number of intermediate files on disk during its operation. If Caret is run in a remotely mounted directory (a disk that is physically on a different computer), this may significantly increase the time required for segmentation.


  1. The volume must be a standard T1-weighted MRI.
  2. The intensities must be consistent throughout the volume.
  3. The volume must be in an LPI orientation. That is, negative X is left, negative Y is posterior, and negative Z is inferior.
  4. The voxel size must be cubic one millimeter for humans and 0.5 millimeter for monkeys.
  5. The stereotaxic coordinates must have the origin (0, 0, 0) at the anterior commissure.
  6. The volume must contain a full or partial hemisphere.
  7. The voxel values must range from 0 to 255.

Altering Volume Attributes in Caret

Movie Showing an Example of Altering Volume Attributes in Caret

View Movie of Attribute Editing

If the volume does not meet the Caret requirements, Caret may be able to modify the volume to correct the problems. Launch the Volume Attributes Editor by selecting Volume Menu→Edit Volume Attributes. In the Volume Selection section, set the Volume Type to Anatomy and verify that the correct anatomical volume is selected. If you make changes to the volume, be sure to save the volume file.

Updating Stereotaxic Coordinates using the Volume Attributes Editor.

  1. Press the Coordinates Tab.
  2. If the Voxel Size does not reflect the size of the voxels in the volume, set the X, Y, and Z sizes of the voxels.
  3. If the coordinate of the first voxel in the volume is known, enter its coordinates in the Origin at Center of First Voxel controls. If not, use the controls in Caret's Main Window to place the intersection of the X, Y, and Z crosshairs on the anterior commissure and press the Use Main Window Crosshairs as AC location button. There are other buttons in the Set Origin section that can set the AC. To see their function rest the mouse arrow over the button and a tooltip will appear.
  4. Press the Apply button.

Voxel Resampling Using the Volume Attributes Editor

  1. Press the Resample Tab.
  2. Enter the desired voxel sizes.
  3. Use Cubic Interpolation.
  4. Press the apply button to resample the volume.

Setting the Volume's Orientation

  1. Press the Orientation tab.
  2. Set the orientation X, Y, and Z controls so that they reflect the orientation of the volume.
  3. If the volume is not in an LPI orientation, use the available buttons so that the volume enters an LPI orientation.
  4. Press the Apply button to apply the changes.

Changing the Range of Voxel Values to 0 to 255

  1. Press the Data tab.
  2. Set the Output Range to 0 to 255.
  3. If needed, the Current Range may be altered to account for outliers (extreme values). Using the Show Histogram button may be helpful identifying outliers.

Intensity Correction in Caret

Caret has a limited capability for correcting inconsistent intensities in the volume file.

Image:CaretSegmentationNonUniform.jpg Image:CaretSegmentationNonUniform2.jpg

  1. Select Volume Menu→Anatomy→Bias Correction.
  2. Set the Gray Minimum to the minimum gray intensity.
  3. Set the What Maximum to the maximum white intensity.
  4. Press the Apply button.

Cropping to a Full or Partial Hemisphere

The segmentation algorithm requires a volume that contains either a full hemisphere or a partial hemisphere.

  1. Select Volume Menu→Resize Underlay Volume.
  2. Use the arrow buttons on the Resize Volume Dialog so that the cropping lines shown in the Main Window tightly enclose the desired full or partial hemisphere. Use the horizontal, coronal, and parasagittal views as needed.
  3. Press the Apply button.
  4. Save this cropped volume to a new file.

SureFit Segmentation

Select Volume Menu->SureFit Operations (Segmentation) to launch the SureFit Segmentation Dialog

Movie Showing an Example of Initial Segmentation Processing

View Movie of Initial Segmentation Processing

Change/Verify Current Directory Page

During the segmentation process, new files will be created. So that the files are saved in the correct location, verify, and, if necessary, update the current directory.

Subject Information Page

The values selected on the subject information page affect the naming of files created during the SureFit segmentation process. In addition, the stereotaxic space is used for a new capability that attempts to automatically draw flattening and registration borders on human subjects.

Spec File Selection Page

Verify that the Spec File name is correct and in the correct location.

Volume Selection Page

The SureFit segmentation process may start with either an anatomical volume or a segmentation volume. If an anatomical volume is input to the algorithm, the cortex will be extracted and a segmentation volume created. A segmentation volume is typically used as input when corrections have been made manually to the segmentation volume prior to surface generation. In some operations, such as automatic border drawing, both the anatomical and segmentation volumes are needed.

In the Volume Selection section, verify that the correct volumes are selected.

Volume File Type Page

Select the type of volume files that are written here. Use of the NIFTI formats is strongly recommended. The NIFTI format is supported by all major neuroimaging software applications.

Volume Attributes Page

If any problems with the anatomical volume are detected, they are listed on this page and highlighted in red.

Set Gray and White Matter Peaks Page

For proper segmentation, the user must identify the gray and white matter peaks. One the left side of the page is a histogram which is a graph that displays the distribution of voxel values in the anatomical volume. In the Peaks section are controls for adjusting the gray and white matter peaks. When the button to the left of Gray is selected, voxels with intensities greater than the selected gray value are displayed in green. When the button to the left of White is selected, voxels with intensities less than the selected White value are shown in green.

Segmentation Operations Page

This page is divided into a section for Anatomical Volume Operations and a section for Segmentation Volume Operations.

When segmenting an anatomical volume, the Anatomical Volume Options are rarely, if ever, changed from their default values. An option is disabled (grayed-out) if it is dependent upon another option that is not selected.

The Segmentation Volume Options are listed below. Items prefaced with AVS should be selected during anatomical volume segmentation. Items prefaced with SVPP should be selected during segmentation volume post-processing (final surface generation).

  • (AVS) Volume Error Correction Method Enables error correction of the segmentation volume. On rare occasions, the graph algorithm will remove a significant part of the cortex. If this occurs, there are two possible solutions. First, one may need to readjust the gray and white matter peaks, especially if gyri appear to touch in the anatomical MRI. Second, change the volume error correction to just the SureFit error correction and be prepared for some manual error correction. The graph error correction algorithm is based on Shattuck, D.W., Leahy, R.M., 2001. Automated graph-based analysis and correction of cortical volume topology. IEEE Transactions on Medical Imaging 20, 1167-1177.
  • (AVS, SVPP) Generate Raw and Fiducial Surfaces Generates raw and fiducial surfaces from the segmentation volume.
  • (AVS, SVPP) Limit Polygons in Generated Surface(s) Creates the surface with the minimum number of nodes needed that does not alter the overall shape of the surface.
  • Correct All Topological Errors in Fiducial Surface If there are topological errors in the surface, a new topology file is generated that eliminates the topological errors. This operation will alter the shape of the surface so it should be used with caution and may be best only when the topological errors are small. This algorithm first converts the anatomical surface to a sphere and extensively smooths the sphere. Next, the surface normal for each node is computed from the average of the surface normals from the triangles that use the node. The surface normal for the node is then compared to a unit vector that starts at the center of the sphere and goes through the node. If the angle between these two vectors is greater than a certain amount, the node is identified as a topological defect. Nodes NOT identified as a topological defect are then tessellated to create a new topology for the sphere and this topology is subsequently applied to the anatomical surface.
  • (AVS, SVPP) Generate Inflated Surface Creates an inflated surface.
  • (AVS, SVPP) Generate Very Inflated Surface Create a very inflated surface.
  • (SVPP) Generate Ellipsoid Surface (for Flattening) Create a very inflated surface that is used by the flattening algorithm.
  • Generate Spherical Surface Create a spherical surface.
  • Generate Compressed Medial Wall Surface Create a compressed medial wall surface.
  • (SVPP) Generate Cerebral Hull Create a surface from the cerebral hull volume.
  • (SVPP) Generate Curvature, Depth, and Geography Attributes Generate surface curvature, depth, and geography paint attributes.
  • Create Flatten and Registration Borders Attempt to automatically generate flattening and registration borders.
  • (AVS, FSG) Auto Save Generated Files Automatically save any files created during the segmentation process.

Segmentation Volume Manual Error Correction

Image:CaretSegmentationErrorCorrectBefore.jpg Image:CaretSegmentationErrorCorrectAfter.jpg

After the segmentation of an anatomical volume, the resulting segmentation volume typically contains errors where voxels were not properly identified. These misidentified voxels cause either topological defects, exclude cortical matter, or include non-cortical matter. To correct these remaining problems, the user must manually edit the segmentation volume to correct the errors.

Tips for Segmentation

  • Use Volume Menu→Segmentation→Topology Error Report to check the selected segmentation volume's topology.
  • Scroll through the slices to look for any obvious errors.
  • Open a viewing window (from the Window Menu). Display VOLUME in the viewing window and select the UO and Yoke buttons. The anatomy volume is shown in the viewing window and the slice is the same as shown in the main window.
  • Use Volume Menu→Segmentation→Find Handles to find any holes (handles) that automatic error correction was unable to resolve.
  • Use Volume Menu→Segmentation→Edit Voxels to edit the segmentation volume (watch the movie below).
  • Use Volume Menu→Segmentation→Reconstruct Into Surface to generate a surface for locating errors.

Movie Showing an Example of Segmentation Editing

View Movie of Manual Error Correction

Segmentation Surface Generation

Movie Showing an Example of Final Segmentation Processing

View Movie of Final Segmentation Processing

Personal tools
Sums Database