From Van Essen Lab
Mapping Volumes to A Surface
Two types of volumes are mapped to surfaces with Caret. Functional volumes typically contain floating point data from fMRI or PET experminents and the results are placed in metric files. Paint volumes contain integer data that are indices into a table of labels. These labels may be a partitioning scheme (Brodmann Areas) or indicate regions of interest.
There are two methods for mapping a functional or paint (label) volume to a surface. If the volume contains individual data, the volume must be mapped to the individual's surface. If the volume contains group results, the volume should be mapped to an atlas.
The steps in mapping a volume to a surface are:
- Selecting the type of volume, functional or paint.
- Selecting the functional or paint volumes. The volume may be volumes loaded in Caret or volumes in disk files.
- Selecting the surfaces used for mapping the volume. The surfaces may be surfaces loaded within Caret or those surfaces in a Spec File. If the surfaces are currently loaded in Caret the resulting metric/paint data will be added to Caret and the user will need to save the file. If the surfaces are chosen from a spec file, the resulting data is written to a metric or paint file.
- Naming the metric or paint file and the columns in the file.
- Choosing the mapping algorithm.
Mapping an Individual's Volume to a Surface
An individual's volume must be mapped to the individual's surface. An individual's surface is created by segmenting the individual's anatomical volume. When mapping a volume to the surface, the volume's stereotaxic coordinates must be the same stereotaxic coordinate system used by the individual's fiducial surface.
Mapping a Group Results Volume to a Surface Via an Atlas
A group results volume should be mapped to an atlas. In the case of human data, we recommend the PALS atlas. When mapping volumes to the PALS atlas, the volumes must be in one of the PALS atlas' supported stereotaxic spaces. At this time, stereotaxic spaces supported by the PALS alas are 711-2C, AFNI, FLIRT, MRITOTAL, SPM2, SPM5, SMP95, SPM96, and SPM99. The PALS atlas can be downloaded from SumsDB. The results of mapping to the PALS atlas must be viewed on PALS atlas compatible files (those having 73730 nodes).
Pages in the Map Functional Volumes to Surfaces Dialog
The pages encountered when mapping volumes to surfaces will vary depending upon selections made during the mapping process.
Data Mapping Type Page
Use this page to select the type of volumes (functional or paint) that will be mapped.
Volume Selection Page
Use this page to choose the volume files that are to be mapped. Press the Add Volumes From Disk button to select volumes that are in disk files. Press the Add Loaded Volumes to select volumes that are currently loaded in Caret. To remove a listed volume, select the volume an press the Remove Selected Volumes button.
If you would like to threshold the volumes, select the Enable Entry of Volume Threshold in the Volume Thresholding section PRIOR to adding the volumes. If this option is selected, a dialog enabling the entry of thresholds is popped up when adding volumes. The thresholds entered will be placed in the metric file for use when viewing the metric data.
Spec File And Surface Selection Page
Use Map to Caret and Map to Spec File when mapping individual data to the individual's surface. Use Map to Caret With Atlas or Map to Spec File With Atlas to map group results to the PALS atlas.
- Map to Caret Press this button to select a surface currently in Caret for mapping the volumes. The resulting metric or paint date is placed in Caret. The user will need to save the metric/paint file.
- Map to Caret With Atlas Press this button to map the volumes using an atlas and a dialog for atlas selection is displayed. The resulting metric or paint date is placed in Caret. The user will need to save the metric/paint file.
- Map to Spec File Map the volumes to a Spec File. A dialog is presented that allows selection of a Spec File and fiducial surfaces in the Spec File for use by the mapping algorithm. The resulting metric or paint file is placed into a disk file.
- Map to Spec File With Atlas Map the volumes to a Spec File. A dialog is presented that allows selection of the atlas and its surfaces. The resulting metric file is placed into a disk file.
- Remove Selected Items Press this button to remove any selected Spec File and Surface targets.
Mapping Surface Selection Page
If the Map to Spec File or "Map to Caret" button on the Spec File and and Surface Selection Page, this dialog is presented. If the Map to Caret button was pressed, this dialog is presented but the Spec File option is not displayed.
Select one or more coordinate files. A metric column is created for each selected coordinate file.
Atlas Surface Selection Page
If the Map to Spec File With Atlas button on the Spec File and Surface Selection Page, this dialog is presented. If the Map to Caret With Atlas button was pressed, this dialog is presented but the Output Spec File option is not displayed.
If mapping to a Spec File, use the Output Spec File controls to choose the Spec File.
Choose the stereotaxic space of the volumes that you are mapping. Next, choose the Atlas which is the surface (left, right, cerebellum) that you are targeting. Lastly, choose the Multi-Fiducial Options.
For best results, use the Show Average Mapping to All Multi-Fiducial Cases.
The Multi-Fiducial Options are:
- Show Mapping to Average Fiducial Surface Maps the volumes to the average fiducial surface (AFM - Average Fiducial Mapping). The surface is an average of the individuals in the atlas. This method is fast but there may be some inaccuracies in the mapping due the averaging process that creates the Average Fiducial Surface.
- Show Average of Mapping to All Multi-Fiducial Cases Maps the volume to all individuals in the atlas and then creates an average of these mappings (MFM - Multi-Fiducial Mapping). This method eliminates any biasing due to individual variability and creates the best results.
- Show Sample Standard Deviation of Mapping to All Multi-Fiducial Cases Creates a metric column containing the standard deviation resulting from mapping the volumes to all of the atlas' individual cases.
- Show Standard Error of Mapping to All Multi-Fiducial Cases Creates a metric column containing the standard error resulting from mapping the volumes to all of the atlas' individual cases.
- Show Minimum of Mapping to All Multi-Fiducial Cases Creates a metric column containing the minimum values encountered when mapping the volume to all of the atlas' individual cases.
- Show Maximum of Mapping to All Multi-Fiducial Cases Creates a metric column containing the maximum values encountered when mapping the volume to all of the atlas' individual cases.
- Show Mapping to Each Multi-Fiducial Case Creates a column containing the results of mapping the volume to each individual in the atlas.
Data File Naming Page
Use this page to set the name of the metric or paint file that will be created. In addition, the names of the metric/paint file columns and comments may also be edited. Double-click a cell to edit its contents. This page will not appear if mapping the data to Caret.
Mapping Algorithm Page
Use this page to choose the algorithm for mapping volume voxels to surface nodes. Some algorithms have parameters that may be adjusted.
During the mapping process, the volume's stereotaxic coordinates are used along the the node's coordinates to determine which voxel the node falls within.
For mapping metric data, Metric Enclosing Voxel or Metric Interpolated Voxel is recommended. Paint Enclosing Voxel must be used when mapping paint volumes.
The algorithms are:
- Metric Average Nodes Each node is set to to the average of the voxel it falls within and the average of its neighbors.
- Metric Average Voxel A cube with each edge NEIGHBORHOOD SIZE millimeters long is centered at the node. The node is assigned the average of all voxels that are contained in the cube.
- Metric Enclosing Voxel A node is assigned the value of the voxel that the node falls within.
- Metric Gaussian This algorithm is explained below.
- Metric Interpolated Voxel A cube the size of the volume's voxel size is centered at the node. This cube intersects the voxel containing the node and parts of neighboring voxels. A weighted average is assigned to the node based upon the cube's intersection with the neighboring voxels. If the node is at the exact center of a voxel, the value assigned to the node would be the same as the Enclosing Voxel Algorithm.
- Metric Maximum Voxel A cube with each edge NEIGHBORHOOD SIZE millimeters long is centered at the node. The node is assigned the maximum of all voxels that are contained in the cube. If the cube contains only voxels with negative values, the node will be assigned the most negative value. If the cube contains any positive values, the node will be assigned the most positive value.
- Metric MCW Brain Fish This algorithm loops through the voxels. For each voxel that is non-zero, the algorithm find the closest node that is within MAX DISTANCE millimeters. If the node's current value is less than that of the current voxel, the voxel is assigned to the node The splat factor essentially smooths the nodes for SPLAT FACTOR iterations.
- Metric Strongest Voxel A cube with each edge NEIGHBORHOOD SIZE millimeters long is centered at the node. The node is assigned the value of the voxel that is furthest from zero.
- Paint Enclosing Voxel The node is assigned the value of the voxel that contains the node.
The Metric Gaussian Mapping Algorithm
The Gaussian algorithm uses applies a “Gaussian weighting” to the node’s neighbors. The Gaussian function is . Two Gaussian calculations are performed. In the first Gaussian calculation, “x” is the distance from the neighboring node to a plane tangent to the surface at the node being smoothed and sigma is Sigma Normal. If the neighboring node is above the plane and greater than Normal Above Cutoff distance from the plane, the neighboring node receives a weighting of zero. If the neighboring node is below the plane and greater than Normal Below Cutoff distance from the plane, the neighboring node receives a weighting of zero. In the second Gaussian calculation, “x” is the distance from the neighboring node to the normal vector and sigma is Sigma Tangent. If the distance from the neighboring node to the normal vector is greater than Tangent Cutoff, the node receives a weighting of zero.
According to http://mathworld.wolfram.com/GaussianFunction.html, Full Width Half Maximum is approximately (2.3548 * Sigma).
Neighbor Box Size A cube this size is placed around the node. All voxels within this cube contribute the the node's value.
Sigma Normal Standard deviation for Gaussian along the node’s normal vector.
Sigma Tangent Standard deviation for Gaussian along plane tangent to the node.
Normal Above Cutoff The cutoff distance in the direction of the node’s normal vector (“Above” a plane tangent to the node).
Normal Below Cutoff The cutoff distance in the direction opposite of the node’s normal vector. (“Under” a plane tangent to the node).
Tangent Cutoff Cutoff distance along a plane tangent to the node.
This page summarizes the selections that have been made. Pressing the Finish button will map the selected volumes to the selected surfaces.
Viewing the Results
To view the results:
- Load the metric file created by the process into Caret along with coordinate and topology files.
- Press the D/C button in the Main Window's Toolbar to display the Display Control.
- Use the Display Control's Page Selection control to the the current page to Overlay/Underlay - Surface.
- Set the Primary Overlay Data Type to Metric. If there are multiple columns of metric data, use the Display Control selection to select other mappings.
There are three types of thresholds.
- Column threshold contains the threshold entered by the user when adding a volume during the Map Volume To Surface or Map Volume to PALS operation.
- Average Area is set when a volume is mapped to the PALS atlas and a threshold (column) is entered for the volume. During multi-fiducial mapping, the volume is mapped to each of the individual cases in the PALS atlas. The threshold is applied to each individual surface and the surface area with metric data exceeding the threshold is calculated on each individual. Next, the threshold exceeded surface areas from each of the individual surfaces are averaged. When the mappings to the individual cases are averaged (creating the Multi-Fiducial-Mapping) a threshold is determined that creates a surface area equal to the average threshold-exceeded surfaces areas of the twelve individuals. This value becomes the Average Area Threshold.
- User is a threshold the user can enter on the Display Control's Metric Settings page.
To use thresholds:
- Go to the Metric Settings page on the Display Control.
- In the Threshold Adjustment section change the Threshold Type to Column.
Mapping Volumes to Surfaces on the Command Line
The program caret_command is used to map volumes to surfaces on the command line. Use caret_command -volume-map-to-surface to map individual data and caret_command -volume-map-to-surface-pals to map group results to the PALS atlas.