Selections

A selection, or label or ROI (region of interest), is a marked or highlighted series of anatomical voxels. The selected voxels can written to or read from an external file and used in different programs.

TkMedit has many specialized methods of creating labels.

Display Options

Voxels that are selected are drawn with a green overlay. This overlay can be turned off by unchecking Views->Selection / Label.

Selecting and Deselecting

Brushing

You can select and deselect voxels with the Select Voxels Tool, which can be activated by pushing the button on the Main Toolbar, by choosing Tools->Select Voxels, or by pressing the 's' key.

This tool is a brush tool, so it uses the global brush settings available in Tools->Configure Brush Shape... and in the Reconstruction Toolbar. You can think of selecting and deselecting voxels as painting your selection on top of the anatomical voxels. Use mouse button 2 to draw your selection and button 3 to erase it.

Flood Filling

You can also use a flood fill to select and deselect contiguous areas. Open the configuration dialog box with the Tools->Configure Flood Select... command. Here, you have options for the making the fill 2D or 3D, settings the source, and the fuzziness and distance parameters.

• Source Volume: Specifies which volume to use when looking for similar voxels, so that the Main, Aux, or segmentation volumes can be used to look for regions. Fuzziness: Determines the level of similarity to consider when finding adjacent voxels to select. If it is 0, only contiguous voxels with exactly the same value as the voxel clicked will be set. If it is greater than 0, this is the maximum value difference from the clicked voxel that a contiguous voxel can have to be considered in the same region. Distance: Determines the maximum size of the region to fill from the clicked voxel. If it is 0, there will be no distance limit. 3D: Determines if the fill is in-plane only or will fill in three dimensions.

Once you have configured your fill, perform it with shift-mouse button-2 or 3; 2 will select an area, and 3 will deselect an area.

In the shell window, you will see a series of dots printed out while the selection is being performed. If it is taking too long, your fill may be filling more than you intended, and may wish to cancel the selection. To do this, make sure the shell window has focus, and enter control-c. Note that the fill will be partially complete even if you cancel, so you may want to clear the selection after cancelling.

Linear Selections

You can use the line tool, , to draw lines that can be turned into selections. Select the tool. Clicking with the middle button will draw a line between the last place you clicked the middle button to the current location. This will draw a green line, with the voxels that intersect the line drawn in red.

Next, select the Tools->Add Line to Selection to select the voxels that intersect the line. You can use this tool to build an accumlation of lines, if, for example, you wanted to build an outline of an area. Or, if you want to just save the current line as a label and nothing else, use the Tools->Write Line to Label... command.

Label Writer Helper

If you want to make a series of collections saved to seperate files, use the dialog brought up by selecting Tools->Label Writer Helper.... This dialog box lets you create a series of label files in a directory with incrementally numbered file names. Select the directory in which to save the labels. Then, choose options for selecting a line before writing the label (if you are making selections based on lines), and clearing the label after writing.

You can have the Helper automatically create label names for you with an incrementing number. Select the Use Incrementing Number for Label Name option, and fill out the three text fields. The first field should be a text prefix for the name. The second should be a number that is automatically incremented. The third is the file name suffix, normally .label. Or, you can specify a list of names to be used with the Get Label Names from File option. Choose a file that has one file name per line. You will see the next file name in the Next name area.

Then, just draw a selection or line and click the Apply button. The label will be written according to your naming specification.

Saving and Loading

TkMedit reads and writes label files. This file format is simply a list of points in RAS coordinate space with some header information. They can be loaded into TkSurfer if they intersect with a surface.

NOTE: If you are using mri_covert and mri_label2vol to create/extract labels, the labels may look very wrong when viewed in tkmedit. This is most likely due to those commands saving the label in a coordinate system that tkmedit does not use. Simply load the label into tksurfer and then save it. The label should now be displayed correctly in tkmedit.