Update Course and Advanced Techniques in MNPS (version 10.36.07, 2019-2020). Functional Neurosurgery Planning Translation into English of the original Portuguese version. MNPS is developed by Mevis Informática Médica, São Paulo, Brazil

1. Update Course and Advanced Techniques in MNPS
(version 10.36.07, 2019-2020)
Functional Neurosurgery Planning
Armando Alaminos Bouza.
Medical Physicist
MNPS/CAT3D Development Team
Mevis Informática Médica LTDA. Brasil

2. -Points based registration: AC, PC, IHP.
-Reformat CT/MRI to parallel atlas maps.
-Commissural coordinate system.
-Identification of the atlas structure that contains the mouse cursor.
-Targets based on commissural coordinates.
-Maps on CT, atlas with MRI fused to CT.
-Graphic representation of the most common electrode models (DBS).
-Electric field model and VTA created by DBS.
Traditionally, the pre-planning of functional neurosurgery procedures
targeting the basal ganglia is done within a stereotaxic space and with
maps created to link nuclei and structures with Cartesian coordinates.
The MNPS has several features specifically oriented to the needs of
functional and stereotactic neurosurgery.
With the introduction of the “Virtual Fiducials” mode, it is important to
understand and be able to use the commissural coordinate system,
even for procedures outside the functional area.

3. The Atlas-Brain registry model is based on reference points.
The classic functional neurosurgery literature is unanimous in the use of the
following points:
AC – anterior commissure
PC – posterior commissure
This geometric information is insufficient for a complete 3D registration. We need
one more point.
The AC-PC line defines rotation around the Z and X axes. It remains to define the
rotation around the Y axis.
Since 1992 (then the system name was NSPS) we have introduced the IHP (inter-
hemispheric point). It marks a point on the mid sagittal plane that defines a triangle
with vertices AC-PC-IHP .
These three points make it possible to register the stereotaxic maps in the patient's
brain. MNPS only enables maps after creating POIs AC, PC, IHP.
Note that the triangle formed by AC-PC-IHP cannot have zero area (0.0). Therefore,
we recommend that the AC-PC and PC-IHP sides form an angle close to 90 degrees.

4. Classical atlas of functional neurosurgery.
There are recent works with novelties in histology, width of sections and
conservation of architecture, one of which is being developed at
Universidade de São Paulo (USP).
Note that different atlas maps have discrepancies between them, as they
were created from different models (autopsy brains). Maps from different
planes, within the same atlas, are also different! Morel has corrections in
this regard (canonical atlas), yet each plane is different from the others
(Niemann et.al., Acta Neurochir. 1994)
Another modern idea is probabilistic functional atlases. One of them is the
LPBA40, which we will discuss later.

5. How to set AC, PC, IHP( 1 )
Example of IHP below AC-PC plane

6. How to set AC, PC, IHP (2)
Example of IHP higher than AC-PC plane

7. z
X
Y
MCP = (0,0,0)
Taken from: “Neurofunctional Systems: 3D Reconstructions with
Correlated Neuroimaging”. By Hans-Joachim Kretschmann,
Wolfgang Weinrich, Wolfram Fiekert
Commissural coordinate system.
Commissural coordinates are a Cartesian system based on AC and PC. In MNPS,
the origin of the system is at the inter-commissural midpoint, also know as
Mid-Commissural Point.

8. After creating the AC, PC and IHP POIs, the MNPS
starts to report the commissural coordinates of the
cursor position.

9. Atlas’ map registered over stereotaxic CT and fused MRI: MNPS contains digital maps
based on classical atlas architecture. We use an internal vector representation that
allows scaling and deforming the maps.
Schaltenbrand - Wahren

10. Atlas Menu : Where is the cursor?
To open “Atlas Menu” use <CTRL-F6> or click on “?”
Until version 10.33.03 this was the only feature to identify a nucleus in the
main window's active map.

11. Atlas Menu : Where is the cursor?
Coronal map.
Until version 10.33.03 this was the only feature to identify a nucleus in the
main window's active map.

12. In version 10.33.04, MNPS started to continuously inform the nucleus on which the
cursor is located. The information is in the window title (“caption of window”)

13. Fine tuning the maps to the actual brain.
NOTE: Previous versions of MNPS did not save these adjustment parameters.
In version 7.36.6 and later the adjustments are saved in the plan.

14. Morel maps registered in the LPBA40 template.
The side maps correspond to Morel brain Hb1.

15. Proposals for common targets in functional neurosurgery.
Five targets are pre-configured in MNPS

16. In addition to the pre-configured targets, the user can create others, according
to their personal preferences.
To do so, you must edit the MNPS.INI file, using an ASCII editor, like NotePad.
Each target must be at the beginning of a line. The syntax is:
FUNCT_TARGET = Xc Yc Zc name_target
Where “FUNCT_TARGET” is a keyword, Xc, Yc, and Zc are the target coordinates
in the commissural coordinates system. Lastly “name_target” is the target
name. Please, do not introduce blank spaces in the target name, use ‘_’ or ’–’ if
needed.
Example:
FUNCT_TARGET = 5.2 9.6 -7.5 Fx-hT
Representing the median of the coordinates used to stimulate the fornix region
according to: “Bilateral deep brain stimulation of the fornix for Alzheimer’s
disease: surgical safety in the Advance trial”, Journal of Neurosurgery
December 18, 2015.

17. Now we have a new target created by the user via the MNPS.INI file:
Axial Coronal

18. The maximum number of targets that MNPS supports is 64. As it comes
preconfigured with 5, the user can define only 59 targets in the
MNPS.INI file, using the syntax:
FUNCT_TARGET = Xc Yc Zc name_target
Remember that while the target name (name_target ) can tolerate up to
32 char, the POI that generates the MNPS for the targets is limited to 8
char. The long name appears in the target selection menu, but the
created POI will have its ID truncated.

19. There are criticisms of the use of targets guided exclusively by stereotactic
atlases. Atlas are based on the anatomy of a model and should not be applied
without adjustments to the patient. Advocates of “direct targeting” based
only on images, usually MRI, must also be careful. Let's take STn as an
example.
AJNR Am J Neuroradiol25:1516–1523,
October 2004

20. Dormont Didier., et.al., AJNR Am J Neuroradiol 25:1516–1523, October 2004
In the Frontal plate, posterior 7mm, the T2 image does not show hypodensity, although
there is still STn in this region.
We consider that correlating the classic stereotactic atlases with the patient's images is
a good practice to avoid errors created by the peculiarity of the imaging techniques or
deviations of the patient from the atlas.

21. How to move the MNPS cursor to a point on the
brain known its commissural coordinates.
It is possible to find references to points of interest or
targets of functional surgery in the literature. If the MNPS
plan has already defined the POIs AC, PC and IHP, the
system can move the cursor to the coordinates Xc,Yc,Zc in
a very simple way.
With the keyboard command <CTRL-X> or from the help
menu (F1) select “Goto Commissural XYZ”.

22. In the example shown, we want to
go 12.0 mm to the right, 1.5 mm
posterior to the “mid commissural
point” and 2.5 mm caudal to the
AC-PC horizontal plane.
MNPS will jump the cursor to
horizontal plane, parallel to AC-PC
plane, with Z=-2.5 and to the pixel
closest to the requested X,Y.

23. The POI’s editor in commissural mode.
Activate with: SHIFT + Click on the POI editor button

24. Showing a functional surgery nuclei in the 3D window

25. Click on the < ? > (help) from the 3D toolbar or directly press the F6 key

26. Select the nuclei you want to show and the display mode, solid or wires

27. Results of 3D nuclei presentations
“wire-frame” mode
“solid”

28. Representation of DBS electrodes
In MNPS, DBS are linked to trajectories. Let's remember how we created
trajectories.
The button indicated on the toolbar starts the creation of a path between a
pre-existing POI and a new POI that we are going to create. The new POI is the
trajectory destination, usually the target.
(Pre-existing POI)
Name for new destination POI

29. If the pre-existing POI is the keyword “OUT” it means that we are going to create the
trajectory based on alpha and beta angles (arc and ring angles respectively). The new
POI is always the distal or deepest point, usually the target.
beta
alpha

30. Alpha and beta angles of the trajectory
Beta
Alfa
A Macom system A FiMe or Bramsys system

31. Another way to create trajectories. With the POI editor.
Create a POI for input and a POI for destination. Open the POI editor. In the “FROM” field
of the destination POI (target point), enter the name of the POI of the entry. In the “Z-Bar”
field, select the position to fix the Z-bar. Close the editor by clicking on [OK].

32. How to accurately represent the location of active
DBS contacts:
• DBS has to be a trajectory.
• The DBS tip has to be the trajectory destination.
• The name of the destination POI must include the
character * (asterisk).
See example

33. How to define the DBS model of the plan.
Variant 1, Via the functional menu:

34. How to define your DBS model (2).
In the MNPS main menu go to “Options” and select “Set DBS Model”
In the window that opens, select the DBS model that you will implant.
As of the date of this class the MNPS
contains 9 models with implemented
geometry, two from Medtronic, four
from Saint Jude, two from Boston and
three from SceneRay. Others will be
added as they enter our market.

35. MNPS showing three DBS models in the 3D window
Medtronic, 1.5 mm spacing - Boston Vercise, Directional - St. Jude 1.5 mm spacing

36. 2D representation of the active contact. The cut that intersects a contact has the
entire diameter filled in gray. Cuts that do not intercept contacts show the DBS
diameter without solid color.
Two examples in axial follow.
Active region Passive region

37. Representation of DBS on 2D sections parallel to them
Note that contacts can be seen superimposed on maps.
(this situation is extremely unusual as the DBS are generally oblique in relation
to the segmented planes in the atlas)

38. The “Probe-View” is the most natural way to present contacts over the anatomy.
But for that you must hide the maps, because the atlases are not parallel to the
Probe-View planes. (Atlas hides or shows with F6)

39. MNPS allows simulating the distribution of the electric
field associated with DBS programming parameters,
within certain limits. The MNPS model uses the finite
element method (FEM) for quasi-static conditions and
assumes isotropic electric properties of the surrounding
tissue.
Open the functional menu, <CTRL-F6>, and select “VTA
Switch” . This switch turns the electric field on and off.

40. If you already have the electrodes activated and
you want to change the programming parameters,
select “DBS: Parameters”
The calculation time varies with the number of
active contacts, the zoom level, the region shown,
and the CPU power installed in the PC.

41. Presentation of the electric field on 2D images. MNPS presents curves of equal
magnitude of the electric field vector, ie |E|. The curves inside the red shaded
area are inside the “Volume of Tissue Activation” (VTA).
The relationship between |E|,
frequency, pulse width with VTA
is based on the literature [5,8,9].
See references at the end.

42. To present the VTA in 3D, simply have the electric field
activated and invoke 3D rendering

43. You can present the VTA superimposed on atlas nuclei, tracts,
ROIs, etc. In this case we show the VTA superimposed on the STn
and we also show the red nucleus.

44. Proposal and implementation of metrics to optimize stimulation with DBS.
GACPC© Algorithm.
Relate the VTA to the volume of the target nucleus or subnucleus of the stimulation.
Use similarity indices such as Paddick Conformity index (PC), Jaccard index (JI) and
Sørensen index (SI).

45. “Proposition of the GACPC© Algorithm for DBS to Optimize Nucleus Targeting and Postoperative
Programming”. Gallani, Nevair(1); Alaminos-Bouza, Armando(2); Carrondo-Cottin, Sylvine(3);
Prud’homme, Michel(3); Cantin, Léo(3); Aguiar, Paulo-Henrique(1). (2018)
(1) Hospital Santa Paula, São Paulo SP, Brazil. (2) Mevis Informatica, São Paulo SP, Brazil
(3) Laval University, Quebec QC, Canada.
GACPC Algorithm has authorship copyright.
Implementation of the
GACPC© in the MNPS
System

46. Registration and use of kinesthetic points in MNPS:
The original idea for this feature was proposed by Dr. Mark Sedrak (Associate Clinical
Professor, Stanford University. Kaiser Permanente, Redwood City, CA). Mark also
provided the three sets of kinesthetic points that we can now test with MNPS.
Kinesthetic points collected by
Dr. Mark Sedrak on trajectories
at STn and projected onto the
LPBA40 atlas’ brain.

47. The points are collected in text files (ASCII), always with the extension “.KPTS”.
We cannot detail the syntax of these files here. We just show as an example
the first lines of the file with trajectories to STn:
YXZ,1, "Dr. Mark Sedrak"
0.065,-12.111,-0.135, 15, 50, 0, 0 ,255, Arm Adduction
-1.629,-11.053,-2.615,15, 50, 0, 0, 255, Arm Adduction
-1.890,-10.890,-2.997,15, 50, 0, 0, 255, Arm Adduction
-1.535,-13.210,-0.685,1, 50, 0, 0,255, Deltoid
....
In the first line we have the order of the coordinates (in the case of Dr. Mark Sedrak,
using CRW, the Y comes before the X). The number 1 indicates that we are going to
read only one property.
Every line after the first contains the three commissural coordinates of the point and a
number that relates its property, in this case the location of the response.

48. To select a kinesthetic points file (the point of interest in general) we use the
keyboard command <CTRL-K>
This command opens a .kpts file selection window.
The <CTRL-K> command is used both in the 2D planning window and in the 3D
window.
Note that kpts files can only be loaded after defining the AC, PC, IHP POIs.
To hide or show the points we simply use the <K> key.

49. MNPS options accessible via the kinesthetic points menu: <ALT-K>
Only Point Cloud Line by least squares Probabilistic ellipsoid

50. We can present KPTS along with trajectories, atlas, 3D and 2D rendering.
Trajectories that run close to the mean line by KPTS regression have a high
chance of modulating regions represented in previous kinesthetic exploration.
The KPTS plot
follows the
same active
spatial
transformation
for the
functional atlas
in use, which
means that the
points appear
normalized to
the patient's
brain.

51. Estimating the extent of lesions created by
Radiofrequency.
This idea was proposed by Application
Engineer Daniel Cosme (Computer
Science), who is participating in this
development.
For now, the results are based on
published tables (see ref.[13,14]).
Future developments will present
graphical results superimposed on 2D and
3D anatomy.

52. Theoretical models for estimating the extent of an RF lesion with the FEM hybrid
method can take 3 hours of calculation on a 3.04 GHz dual Xeon station [13]. This
degree of complexity forces us to base the project on experimental results in vivo
and in vitro [14].

53. How to use the LONI LPBA40 (possibly others with the same
methodology).
- Import the LPBA40, with our Dicom importer, which also
supports NIfTI. Do this for the “template” and “label” volume.
- Create new plan for both volumes.
- Create POIs for registration by POIs in the template volume.
- Export both image sequences for fusion.
- To register a real brain, mark the same POIs you used in the
template (there must be more than 4 POIs).
- Start the fusion, which will be done by POIs. It is very likely not
reach a good fusion, as they are totally different brains.
- Go back to the fusion menu (ALT-F5) and change the rigidity
modulus to 256, in order to deform the LPBA40 for better
agreement with the real brain. That is, using a non-rigid image
registration and fusion.

54. • Close and reopen the fusion (F5 followed by another F5). Now the
recording was done with the LPBA40 deformed to approximate the real
brain.
• If you are satisfied with the result of the registration / fusion, go to the
fusion menu and select: “Load Sequence with Same Registration”.
Choose the volume of “LABEL”.
• Click on the Brightness and Contrast button.
Press the P key until the text “LPBA40-Colors” appears in the title of the
windows window (caption). With this, the MNPS activates the identification
of structures by the identification code of structures of the LPBA40.

55. Using the <M> or <CTRL-M> key, modify the transparency level of the LPBA 40
to observe the real brain anatomy.
without MIX with MIX

56. Example with cursor over cingulate gyrus. The label of the structure appears on Window’s caption.

57. Note that wherever
you place the MNPS
cursor (with click) the
system indicates the
name of the structure
according to the
LPBA40 associated
label. The name is in
the caption of the
window.

58. Planning and post-plan of Stereotactic electroencephalography (sEEG) implants.
MNPS has several build-in sEEG electrode models that allows the graphic representation of
each contact inside the patient’s brain.
As it is the case of DBS, each sEEG trajectory must contains the character * (asterisk) to be
treated and represented as an electrode.

59. Graphic representation of a DIXI with 12 contacts. The left upper screenshot is the
2D axial rendering of the sEEG. The other two images are 3D rendering of the DIXI.
The left lower figure is a detail of the 3D scene at the right side.

60. Bibliography :
1. Niemann K., et.al. “Verification of Schaltenbrand and Wahren Stereotactic Atlas”, Acta Neurochir (Wien) 1994
2. Dormont Didier., et.al., “Is the Subthalamic Nucleus Hypointense on T2-Weighted Images? A Correlation Study
Using MR Imaging and Stereotactic Atlas Data”, AJNR Am J Neuroradiol 25:1516–1523, October 2004.
3. Haus, Hermann A., and James R. Melcher, “Introduction to Electroquasistatic and Magnetoquasistatic”.
Electromagnetic Fields and Energy. (Massachusetts Institute of Technology: MIT OpenCourseWare). Prentice-
Hall, 1989.
4. Gabriel C., et. Al., “The dielectric properties of biological tissues: I. Literature survey” . Phys. Med. Biol. 41
(1996) 2231–2249.
5. Mädler B., et. al., “Explaining Clinical Effects of Deep Brain Stimulation through Simplified Target-Specific
Modeling of the Volume of Activated Tissue”. AJNR Am J Neuroradiol 33:1072– 80. Jun-Jul 2012.
6. Choi C.T.M., et.al., “Modeling Deep Brain Stimulation Based on Current Steering Scheme”. IEEE TRANSACTIONS
ON MAGNETICS, VOL. 47, NO. 5, MAY 2011 .
7. Schmidt C., “Influence of Uncertainties in the Material Properties of Brain Tissue on the Probabilistic Volume of
Tissue Activated”. IEEE Trans. Biol Eng. Vol 60., No.5 2013.
8. Butson C.R., et.al., “Sources and effects of electrode impedance during deep brain stimulation”. Clinical
Neurophysiology, 117 (2006).
9. Butson C.R., et.al.,“Patient-Specific Analysis of the Volume of Tissue Activated During Deep Brain Stimulation”.
Neuroimage, 34(2):661-670 (2007).
10. Frankemole A.M.M, et.al. “Reversing cognitive–motor impairments in Parkinson’s disease patients using a
computational modelling approach to deep brain stimulation programming”. Brain 2010: 133; 746–761.
11. David W. Shattuck, “Construction of a 3D probabilistic atlas of human cortical structures”. Neuroimage vol.39,
Issue 3 (2008).
12. Laboratory of Neuro Imageging. «LONI Probabilistic Brain Atlas (LPBA40)»
http://loni.usc.edu/atlases/Atlas_Detail.php?atlas_id=12
13. Thermal modeling of lesion growth with radiofrequency ablation devices. Isaac A. Chang, et.al. BioMedical
Eng. Online, 2004.
14. In vivo and in vitro study of lesions produced with a computarized radiofrequency system. Vina F.C, Zamorano
L., et.al. Stereo. Funct. Neurosur. 1992.

61. Summary :
Targeting for functional neurosurgery depends on the location of POIs: AC,
PC, and IHP. These points are the basis of the atlas-brain registration and
the commissural-brain coordinate registration.
It is the operator's responsibility to create the POIs: AC, PC and IHP. There is
no automatic way to create these POIs in a safe way.
After creating the aforementioned POIs, MNPS makes available to the user
a large number of functional tools: several vector atlases, DBS
representation, commissural coordinates, KPTS, sEEG representation, and
more.