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Labels, or ROIs, are collections of vertices that can be treated as a group for various applications. In TkSurfer, you can use labels to get average values for overlays or time courses. You can also export label files for use in other FreeSurfer programs, or export a collection of labels as an annotation.

TkSurfer can have multiple labels, each with a different designation. Labels in TkSurfer can be associated with anatomical areas or just be given a color for display purposes. TkSurfer has drawing and filling tools to assist you in creating new lables based on surface data.

The label file format is interchangable with TkMedit. You can create a label in TkSurfer, save it, and load it in TkMedit, or vice versa.

Loading Labels

Use File->Label->Load Label... item to load an individual label file. A label file is a list of RAS coordinates and associated vertex indices that make up the label

You can also import an annotation file as a series of labels. An annotation file is a binary file that assigns a label index to each vertex in a surface. When the annotation is imported, a label is created for each unique index, and the vertices with those values are added to that label. This can be done with the File->Label->Import Annotation... command.

Saving Labels

Use File->Label->Save Label command to overwrite the original file, or File->Label->Save Label As... to save a new label file in a new location. the current dipole values.

Labels Window

Creating Labels

Drawing lines


Erasing lines

Marked Vertices and Labels