There is not a direct way to draw contours over volume slices in Caret but you can try the following method:

1) Display your volume in the Main Window with the slice set to one containing the lesion. 2) Select File Menu->Capture Image of Main Window. Set the Capture Type to "All or Main Window Graphics Area" and check the Add to Loaded Images checkbox in the Image Destination group.
3) Press the Capture button on the Capture Main Window Image Dialog.
4) Increment to the next volume slice in the Main Window.
5) Repeat steps 3 & 4 until images have been captured of all slices the contain the lesion.
6) Select Layers Menu->Contours->Create New Contour Set.
7) Press the D/C button in the Main Window Toolbar to launch the Display Control Dialog. Set the Page Selection to Images which should list the images of the volume slices captured in steps 3&4. Check the Show Image in Main Window checkbox so see the first image in the Main Window. 8) Select Layers Menu->Contours->Draw Contours, set the contour number (perhaps using the stereotaxic coordinates shown in the bottom left corner of the volume image), and draw a contour around the lesion.
9) On the Display Control's Images Page, select the next image.
10)Repeat steps 8&9 to draw the remaining contours around the lesion.

It will also be necessary to use Layers Menu->Set Contour Scale to set the proper X/Y scale of the contours and Layers Menu->Set Contour Section Spacing to set the distance between the slices.

Another method to identify the lesion is to create a segmentation volume.

1) Select Volume Menu->Create New Volume. Set the Type to Segmentation and enter a Name for the segmentation volume such as "lesion". Press the Set Attributes Using Volume File and select your anatomical volume containing the lesion so that the new volume has identical dimensions, voxel size, etc as the anatomical volume. Press the OK button on the Create New Volume Dialog. 2) Press the D/C button in the Main Window Toolbar to launch the Display Control Dialog. Set the Page Selection to Overlay/Underlay Volume. Set the Underlay to your anatomical volume and set the Primary Overlay to the Segmentation Volume you created in step 1. 3) Select Volume Menu->Segmentation->Edit Voxels. Set the Editing Mode to Turn Voxels On, adjust the Brush Size if desired, and press the Apply button. 4) Place the mouse over the lesion, hold down the left mouse button and move the mouse so that the lesion is covered with segmentation voxels (dark red color).
5) Increment to the next slice containing the lesion.
6) Repeat steps 4&5.
7) Save the Segmentation Volume using File Menu->Save Data File. Set the File Type to a Volume File and at the bottom of the dialog, set the Volume Type to Segmentation. Press the Save button. 8) Select Volume Menu->Segmentation->Reconstruct into Surface. The Surface Type may be set to Brain Model Surface which will generate a caret surface from the segmentation voxels or VTK Model. You can only view one Brain Model Surface at a time within Caret. There is no limit to the number of VTK models you may load into Caret but they are only shown when a fiducial surface is displayed. VTK models are controlled on the Models page of the Display Control Dialog. Press the OK button.

John Harwell

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave.    Box 8108
St. Louis, MO 63110   USA

On Nov 20, 2006, at 9:55 AM, Andrew Reid wrote:

In addition, is there any way to draw contours directly onto volume sections, or otherwise select voxels from a volume, i.e., to delineate a lesion from a structural MRI volume?

Andrew Reid
Department of Cognitive Neuroscience
Radboud University Nijmegen Medical Centre
Postbus 9101, 6500 HB Nijmegen
The Netherlands

phone +31 24 3666171

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