Using OsiriX for visualizations

To use OsiriX to create much higher quality images than the Scanco software is able to produce, first you

must export a set of DICOM files using the Scanco Evaluation software. This is script 25 or 29 depending

if you’re on the MicroCT 40 or Viva. You have two choices when using this script – export either just the

VOI that contains your contour, or export the full scan.

To generally duplicate what most people are used to doing in the Scanco software, simply draw

squares/circles around your general volume of interest, morph between them, and then hit the

Default VOI button.

To export the entire scan, type the number 1 in the left had columns next to the Default VOI

button and 9999 in the right hand columns (it will automatically adjust downward to the

maximum possible value).

If you have a scan with multiple bones, it is best to export the full scan and then use the DICOM cropper

program in MATLAB available on the Dell. This is because the names of the files can get all jumbled due

to how OpenVMS marks filenames with ;1, ;2, ;3, etc if you try to export multiple sets using the Scanco

software, whereas the MATLAB script neatly puts each bone in its own folder.

Once you have exported a set of DICOMS you will need to retrieve them. To do this, go to the Dell and

make a folder on your flash drive or external hard drive whose name is your sample number (ex:

00000345). Next, run either getDicomFromViva.exe or getDicomFromMicro.exe as appropriate. Type in

your three or four digit sample number, give it a starting measurement number (or 00000 for all

measurements), point it to the folder you created, and let it run until it has copied all of your files. If you

exported DICOMS for a lot of measurements or you did high res scans this may take a while.

Unfortunately if a progress bar is added to this program it will blink a lot and is very annoying; once the

appropriate number of DICOM files has been copied to the last measurement folder on your flash drive

it has completed.

Note that running this script deletes the DICOM files from the CT server after they’re copied

over, and this is on purpose. If you use another method to copy your DICOM files over you

MUST delete them after they’re copied. Do not expect your DICOM files to be saved on the CT

server, as they will not be.

Once the files have finished copying, take them to the Mac.

On the Mac, open OsiriX. Once open, click Import in the upper left and direct it to the folder with the

DICOM files you’d like to make an image from.

When prompted, click copy links.

Once it’s done importing (there’s a status bar in the lower left), highlight the appropriate study in the

main list, then double click the image in the lower left. It will prompt you saying it can’t be used for

medical diagnostics, say ok.

If prompted, click resample.

Now, click 3D on the top menu bar and select 3D Volume Render.

It will render the entire contents of the DICOM files. To change the threshold of what it displays, click

the black square in the upper left, then left click in the image, hold it down, and SLOWLY move the

mouse around. Try the other buttons to see what they do.

When you find a set of WW/WL values that works, write them down for use with the rest of your

samples. You can set these manually in future samples.

To export an image, go to file -> export -> tiff and name as desired.

To make a simple rotating movie, click movie and set as you desire. To create a flythrough, click the

arrows on the top right of the screen and click fly thru. Set sequential frames by manipulating the object

and hitting the plus button, then click movie, compute, play it, and save if desired.

Then import your next set of data, navigate to the 3D Volume Render, click WW/WL, manual. Type in

the numbers you wrote down and the color scale will be the same as before. Jet is the CLUT people tend

to favor for heat maps, otherwise play around! Don’t forget to set the rendering settings to finest and

try the GPU engine as well.