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
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.
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?
Department of Cognitive Neuroscience
Radboud University Nijmegen Medical Centre
Postbus 9101, 6500 HB Nijmegen
phone +31 24 3666171
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