Caret6:Documentation/UserInterface/MapVolumeToAtlasWindow

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Contents

Map Group Volume via Atlas to Surface

This window is used to map functional and label volumes containing group (average of multiple subjects) data to via a surface-based atlas to surface metric and label files.

Data is entered on a series of pages so that the volumes can be mapped.

Select Data Type Page

Data Mapping Type

  • Label (Region of Interest) Data - Select if mapping a label volume.
  • Metric (Functional) Data - Select if mapping a functional volume.

Choose Volumes Page

Volume Files

  • Add Loaded Volumes - Pops up a dialog for selection of loaded functional or label volumes for mapping.
  • Add Volumes From Disk - Pops up a file selection dialog for adding volumes that are on the disk. Multiple volume may be selected by using control and shift keys.
  • Remove Selected Volumes - Removes any volumes that are selected.

Thresholding

  • Enable Entry of Thresholds - If selected, thresholds may be entered that will be added to the mapped metric column's color mapping parameters.

Choose Atlas Page

Mapping Atlas

  • Atlas - Selects the target atlas.
  • Space - Selects the stereotaxic space of the volume data that is being mapped.

Structure - Lists the structures that are available for the selected Atlas and Space combination.

Choose Atlas Mapping

Metric Mapping

  • Average Anatomical Mapping (AAM) - Maps the volume(s) to the Average Anatomical Surface. The Average Anatomical Surface is typically created by averaging the individuals that make up the atlas.
  • Multi-Anatomical Mapping (MAM) - Maps the volume(s) to all individuals in the atlas and then averages the results.
  • Standard Deviation of MAM - The standard deviation of mapping to all individuals in the atlas.
  • Standard Error of MAM - The standard error of mapping to all individuals in the atlas.
  • Minimum of MAM - The minimum value at each node from mapping to all individuals in the atlas.
  • Maximum of MAM - The maximum value at each node from mapping to all individuals in the atlas.
  • All Individuals of MAM - Outputs additional metric columns that contain the mapping to each individual case in the atlas.

Label Mapping

  • Average Anatomical Mapping - Map ths volume(s) to the Average Anatomical Surface. The Average Anatomical Surface is typically created by averaging the individuals that make up the atlas.
  • Most Common of Mapping to Multi-Anatomical - Maps to all individuals and assigns the label most common to each node.
  • Most Common (Exclude Unknown) of Mapping to Multi-Anatomical - Maps to all individuals and assigns the label most common, but not the unknown label, to each node.
  • All Individuals of MAM - Outputs additional label columns that contain the mapping to each individual case in the atlas.

Notes

In the PALS atlas, the cerebellum contains a single subject. In the event that AAM is not selected but MAM is selected, the algorithm will map data to the cerebellum using AAM.

Choose Mapping Algorithm Page

  • Metric Enclosing Voxel - Map a metric file by assigning the node's metric value the value of the voxel that contains the node.
  • Label Enclosing Voxel - Map a label file by assigning the node's the label from the voxel that contains the node.

Map to Surface Page

Pressing the Next button will map the volumes to the surfaces. If any errors occur during the mapping process, an error message dialog will appear. Depending upon the files selected, this process may take up to several minutes.

Data File Saving Page

This page is used to save the label and metric files that were created. When the Finish button is pressed the files are loaded and/or saved and then the window closes.

  • Load Into Caret - If checked, the label/metric file will be appended to data in Caret. These checkboxes are disabled if there is no surface loaded with a structure matching that of the target surface.
  • Save to File - If checked, the label/metric file will be saved to the file name in the Data File Name text field.
  • Data File Name - Name of the data file used for saving a file.
  • Choose Data File Name - Pressing this button pops up a file selection dialog for choosing the name of the label/metric file. The selected file name is inserted into the Data File Name column text field.
  • Edit Column Data - Pressing this button pops up a dialog that allows one to edit the names of the label/metric columns, the column comments, the columns' study metadata link, and the NIFTI Intent.
  • Target Surface - Listed the surface that was used to map the data.

Structure of Data Files in the Atlas

The surface-based atlas data files are located in the JAR file SurfaceAtlases.jar that is included with the caret distribution. The files are placed in a specific data structure so that additional atlases and/or structures may be added without having to modify the caret source code.

The directory tree for the atlas files is:

  • ATLAS-NAME - Name of the atlas.
    • SPACE - The files for each stereotaxic space are contained in a directory that is the name of the stereotaxic space.
      • STRUCTURE - Each structure is contained in a directory that is the name of the structure.
        • TOPOLOGY - Contains the topology file and MUST be named TOPOLOGY.
        • AVERAGE - Contains the average coordinate file and MUST be named AVERAGE. If there is no average coordinate file, this directory should not be present. This average coordinate file is used for Average Anatomical Mapping.
        • INDIVIDUALS - Contains the individual surface that make up the atlas and MUST be named INDIVIDUALS. These individual files are used for Multi-Anatomical Mapping (MAM). Note that if any structure in a space has individuals, all structures in the space must have individuals.
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