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Getting Started with MNPS.

1. Copy all DICOM images of the patient in a folder in c:\MNPS\dicom\ . Example, if the patient has the name "John Doe", create the C:\MNPS\dicom\John_Doe. Creating a subfolder for each kind of images, CT, MRI, etc.

2. If it is a simple biopsy, without merging with MRI, drag one (1) CT file (stereo-CT) and drop over

the icon (shortcut) of MNPShell on the desktop:

3. Answer if the image belongs to a stereotactic images set. In the case of stereo-CT, answer YES. Open the DICOM filter, which will do the images pre-processing to save them in the internal format of MNPS (*.IMG).

4. If the images are scattered across several subdirectories, use the third toolbar icon and navigate

through the folders until the base of the subfolders containing all DICOM images. Then click on "File" and select "Scan Path in Depth".

5. At any time, you can change the number of images on the screen by viewing an image at a time

or a mosaic with several pictures. To do this you can click on the fourth button from the toolbar or the View option from the main menu. This is a matter of user preference.

6. Sort images on the sequence according to the orientation relative to patient anatomy. Click in

Options from the main menu and select “Sort images”.

Select the sorting criteria according to image orientation.

Axial (transverse) images must be sorted by Z, coronal by Y and sagittal by X. CT images are always in axial orientation. The program will sort the images. Next, if the sort is satisfactory, click "Exit sort".

7. The images are all initially selected to be processed and converted to IMG format. However, you

may need to discard some images for different reasons. In general, it is recommended to dispose, where possible, images with artifacts caused by frame and some images where the

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fiducials are completely united. To deselect a picture, make a click on it and hit the Space key. Space select or deselect a frame. You can also deselect or select by clicking in a blue small square on the right upper corner of each image.

8. To adjust the field of view (FOV), click the icon with a square in dotted line (the fifth icon on the toolbar, shown below). Leave the red frame slightly larger than the fiducials. To accept the FOV, press ENTER.

The selected FOV applies to all images, therefore, it is recommended to go through the set of images checking if in all of the fiducials are within the FOV. 9. IMG images files will be created with names derived from the name of the patient. If you need to

change this name, use “Options”, from the main menu and select “Rename”.

10. When finished selecting DICOM images, adjust FOV, etc., click the floppy disk icon, the system will save the images (*.img) and ask if should call the MNPS to start the search of fiducials: "Call MNPS with this patient?" Reply YES.

11. The MNPS opens asking how the placement of fiducials was made, the frame type, etc. (only for stereotactic systems with several fiducials model or fiducials that could be fixed in different positions). Reply all and click OK. After that the system ask for confirmation. If it is correct, confirm with OK.

12. Beginning search of fiducials. The MNPS tries to find them automatically, but the user must

confirm with <ENTER> if it is right or <ESC> if it is wrong. Watch very carefully each image until complete.

13. The system prompts you to save the data planning. Fill in the fields as required and confirm with

OK.

14. From here each image is properly calibrated and registered to the stereotactic coordinates. The MNPS goes to the image mosaic. Double-clicking an image.

15. If it is for a biopsy and only needs coordinates of the target, just search the image with the best

point for biopsy and click on the desired place. Cursor coordinates will be in the lower right corner as X, Y, Z. To navigate through the images using the arrow buttons or the PageUp / PageDown keys on the keyboard.

16. Create a point of interest (POI) for the biopsy location. Click on the desired place for biopsy and

click the "POI" button on the right side of the toolbar. Give a name for the POI.

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17. To view the coordinates of the POIs open the POI table on the icon that is at left side of the POI icon. To print the POI table click the printer icon that is underneath the icon mentioned above, select "POI Table".

18. To create a POI at the end of a needle trajectory click the icon that looks like a path, next to the

POI table icon.

19. Save the plan by clicking the icon that looks like a floppy disk.

How to merge the previous planning CT with an MRI set of the patient. Image registration and fusion.

20. Drag one (1) DICOM file from MRI and drop on the MNPShell icon.

21. Reply that it is not a stereotactic set of images, as they were made without fiducials.

22. The system will display the images of the first sequence found. As in MRI can be several sequences, you should use the File / Open option or click the corresponding button on the toolbar to display the list of sequences available for the patient and select the one that will be used for registration and fusion. In the list, click on the desired sequence. Images of that sequence will be displayed.

23. For MRI sequence is always necessary to order the images using Options / Sort images by

selecting the "Select sort criteria" as according to plane orientation, whether sagittal, coronal or transverse.

24. Select or deselect images, with space bar. Adjust FOV if necessary.

25. Finish saving changes by clicking the floppy disk icon.

26. CAT3D program will be called because these images does not contain fiducials and the MNPS

only works with stereotactic images. Answer YES to the question "Call CAT3D with this patient?"

27. CAT3D starts. To the question "Do you need image alignment" answer "No".

28. The system prompts you to save the planning. Fill in the fields as required and confirm with OK.

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29. The CAT3D starts by the mosaic. Double-click an image to enter the main window where you can select POIs and draw ROIs if necessary. Click the EXIT icon or press <ESC> key.

30. Go to File menu and select "Export for Fusion."

31. Return to MNPS. Click the icon that looks like a split axial image or <F5> key. You will see the

list of previously imported sequences. Select the sequence that will be used for Registration and fusion.

32. Leave MNPS optimize the fusion for a while until it tells that ran up to 8 times without improvements, and watching the side window that the consistency of the borders between the two image modality is satisfactory. To finish optimizing use <ESC> key. An informational window appears with the results of the fusion Press ESC to close it.

33. To set the area where the MRI is displayed, use <Ctrl-F5>. You will see a red rectangle that

defines the region where the MRI image will be displayed beside CT. This rectangle can be dragged with the mouse by clicking the circle in the center of it, and resized by dragging the lower right corner. You can also move the rectangle with arrow keys, and change the size with numeric key <+> and <->. Press <ENTER> to fix the rectangle position.

34. On the merged image (MRI + CT) you can define POIs and view the coordinates in the manner

already explained above. The coordinates on the registered MRI are transformed into stereotactic coordinates continuously.