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Overlays

Page history last edited by PBworks 13 years, 2 months ago

(1) For the purpose of illustration, let's assume that you have a Z map in your tutorial directory named Z.simple.RealWord-FalseFont.img, and that you ran Cluster Detection on this Z map, generating a 16-bit integer Cluster Mask named Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.img.

 

Run the following command:

 

ThresholdOverlay.csh Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.img Z.simple.RealWord-FalseFont.img

 

This will generate an overlay named Overlay.Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.hdr; note that the program will spit out text to the screen, among which is a line that reads:

 

ThresholdOverlay.csh: output written to ./Overlay.Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.hdr

 

It also outputs lines that read:

 

Load this into MEDx and apply the Color LUT /export/w/apps/tcl/DeactAndActOverlays.lut

Or load this into VolView and apply the Appearance Settings file /export/w/apps/tcl/DeactAndActOverlays.vvt

 

This is useful information.

 

(2) Bring up MEDx, and open up a New Folder.

 

(3) Load in the Overlay image you created in step 1.

 

(4) Select Display --> Apply LUT.... (A "LUT" is a lookup table.)

 

(5) In the Apply LUT, click on the Load LUT button.

 

(6) In the Select A File dialog box, browse to the file named

 

/export/w/apps/tcl/DeactAndActOverlays.lut

 

Make sure that it appears in the entry box entitled Selection:. Then click on the OK button. This will cause the activations to appear in color in the overlay.

 

(7) Let's make a screen grab. Click once on the ZOOM out button (the one where the OM in "ZOOM" is small, not large). This makes the slices smaller.

 

(8) Resize the MEDx window so that it shows six rows of slices, with 10 slices per row. Make sure that slices 0-59 are showing.

 

(9) In the main MEDx window, select Setup --> Printer Setup.

 

(10) In the Printer Setup window, under Type of Printer, select TIFF. Set File Name to point to a TIFF file in your tutorial directory, e.g.

 

/export/w/myHomeDir/tutorial/Overlay.Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.Slices0-59.tif

 

Note that this file name encodes not only the name of the overlay, but also the slices displayed. It may help to widen this window. Then click on the Apply (not OK!) button.

 

(11) Back in the MEDx folder, select Page --> Print Page. This causes a screen grab of slices 0 - 59 to be printed out to the TIFF file you chose.

 

(12) Scroll down the slices in the MEDx folder so that slices 60-119 are now showing.

 

(13) In the Printer Setup window, under Type of Printer, change File Name to

 

/export/w/myHomeDir/tutorial/Overlay.Cluster.Z.simple.RealWord-FalseFont._2.33._0.05.Slices60-119.tif

 

e.g., then click on the Apply button. (You have to click on the Apply button, otherwise your previous TIFF image will be overwritten with the wrong slices!) This causes a screen grab of slices 60 - 119 to be printed out to the TIFF file you chose.

 

(14) Similarly make a screen grab of slices 120-179. (We can ignore slices 180-182 because they're empty.)

 

(15) Exit MEDx. You can now load the three TIFF files that you created into Adobe PhotoShop. I usually change them to JPEG format in Adobe PhotoShop.


 

The final step is 3D Renderings in VolView.

 

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