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fScan Reference Manual, Chapter 1 (Topics): Tutorial
Step 7: 3-D Surface Generation
Create a 3-D surface reconstruction from the scan images.
7.1 Open bia3_7335_1_300.
7.2 Select the 3-plane view from the View taskbar, and darken the image slightly for a better contrast.
7.2 Open the Stats taskbar.
7.3 Select the “ROI surface reconstruction” icon. This will open a new window, labeled 'Brain' with a copy of the bia3_7335_1_300 image.
7.4 Using your arrow, click and drag to create a box around the brain. The box will have a green frame.
7.5 Click and drag the frame to adjust the box, so it contains all of the brain.
7.6 Hit 'Enter'. A new window will appear, also labeled 'Brain' and with an image of the ROI outlined in red.
7.7 Lower the brightness for a better view. The box will have instructions in the top left-hand corner, to 'Click inside Gray Matter region'. With the brightness lowered, a gray matter region should be apparent around the edges of the brain.
7.8 Select the gray matter region and then hit 'Enter'. Now the brain is outlined in yellow and red.
7.9 Select the “Adjust edges” icon from the Stats taskbar. To adjust, simply use the up and down arrow for the yellow region, and the left and right arrow for the red. No adjustments should be necessary.
7.10 Hit 'Enter'.Now the image is shown in red and orange.
7.11 Select the “extract threshold mask” icon in the Stats taskbar. A new window will open with a yellow image of the brain.
7.12 Follow the instructions stated again in the upper left-hand corner and select any of the yellow are within the brain.
7.13 Hit 'Enter'.
7.14 Click the “erode mask” icon on the Stats taskbar. The yellow outline of the skull will disappear, leaving only the image of the brain.
7.15 Select the “grow mask” icon. This will isolate the segment and dilate it. No change will be noted on the image, however.
7.16 Select the “Put mask” icon. The red and orange image of the brain will be brought to forefront again, now with the eroded and dilated image reimposed upon it. No change will probably be noted.
7.17 Select the “make mask” icon. The process will take a few seconds to smooth and generate the surface reconstruction. After a moment, a new window will open, with the generated 3-D reconstruction of the anatomical image.
7.18 Move the reconstruction to your liking using tools in the new Surf View taskbar.
*Note: Depending on how you accessed your current directory, the response time of the adjustments may lag slightly so don't be put off if it takes a moment to translate the adjustment commands to the image.
7.19 Select the 'Save' icon in the File taskbar and type in wmsurf in the window that appears. This will save the surface reconstruction to your current directory as wmsurf.
See Also:
