FIELD

[0001] The present disclosure relates to methods and systems for determining dimensions intra-operatively for fabrication of an artificial bone flap. More particularly, the present disclosure relates to methods and systems suitable for use in craniotomy procedures, including image- guided medical procedures.

BACKGROUND [0002] Craniotomy procedures involve the creation of an opening in a patient's skull, in order to access the patient's brain . The closure of this opening typically involves replacing the bone flap, which was removed to create the opening, back into the opening. However, the need to preserve the bone flap may be problematic as the bone flap may have been fractured or otherwise damaged during removal and/or may not have been removed as a single piece. Any structural damage to the bone flap may compromise patient healing. Inadvertent contamination of the bone flap may also occur during the procedure, which, if not properly detected and treated, may lead to infection of the patient. [0003] Further, craniectomy procedures typically do not involve preservation of the bone flap. Thus, it may be useful to provide a way to fabricate an artificial bone flap when it becomes desirable later to close the craniectomy opening.

SUMMARY [0004] In some example embodiments, the present disclosure provides a method for calculating, in a processor, dimensions for fabricating an artificial bone flap, the method may include: obtaining, using a portable three-dimensional (3D) scanner, intra-operative data indicating dimensions of an opening in a portion of the patient's skull, the intra-operative data including a 3D surface scan of the portion of the patient's skull including the opening and including a first plurality of reference points located on or near the patient; obtaining a 3D reference image of at least the portion of the patient's skull without the opening, the 3D reference image including a second plurality of reference points that at least partly overlap with the first plurality of reference points; calculating 3D dimensions of the opening using the intra-operative data, the intra- operative data being registered to the reference image on the basis of the overlapping reference points; and storing, in a memory in communication with the processor, the calculated 3D dimensions for fabricating the artificial bone flap by a fabrication system.

[0005] In some example embodiments, the present disclosure provides a method for calculating, in a processor, dimensions for fabricating an artificial bone flap, the method may include: obtaining intra-operative data indicating dimensions of an opening in a portion of the patient's skull; obtaining a three-dimensional (3D) reference image of at least the portion of the patient's skull without the opening; calculating 3D dimensions of the opening using the intra-operative data, the intraoperative data being registered to the reference image; and storing, in a memory in communication with the processor, the calculated 3D dimensions for fabricating the artificial bone flap by a fabrication system .

[0006] In some example embodiments, the present disclosure provides a system for calculating dimensions for fabricating an artificial bone flap, the system comprising a processor configured to execute instructions to cause the system to carry out the methods described herein .

[0007] In some example embodiments, the present disclosure provides a computer readable product for calculating dimensions for fabricating an artificial bone flap, the computer readable product comprising computer-executable instructions that, when executed, causes a computer system to carry out the methods described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0008] Reference will now be made, by way of example, to the accompanying drawings which show example embodiments of the present application, and in which :

[0009] FIG. 1 shows an example navigation system to support minimally invasive access port-based surgery;

[0010] FIG. 2A is a diagram illustrating system components of an example navigation system;

[0011] FIG. 2B is a diagram illustrating use of a tracked pointer in an example navigation system;

[0012] FIG. 3A is a flow chart illustrating an example method involved in a surgical procedure using the example navigation system of FIG. 2;

[0013] FIG. 3B is a flow chart illustrating an example method of registering a patient for a surgical procedure as outlined in FIG. 3A;

[0014] FIG. 4 is a diagram illustrating the registration of virtual and actual coordinate frames in an example navigation system; [0015] FIG. 5 shows a block diagram of an example system configuration, including a control and processing unit and external components;

[0016] FIG. 6 is a diagram illustrating the layers of tissue

encountered during a craniotomy procedure; and [0017] FIGS. 7A and 7B are flowcharts illustrating an example method for determining dimensions for fabricating and artificial bone flap.

[0018] Similar reference numerals may have been used in different figures to denote similar components. DESCRIPTION OF EXAMPLE EMBODIMENTS

[0019] The systems and methods described herein may be useful in the field of neurosurgery, including oncological care, neurodegenerative disease, stroke, brain trauma and orthopedic surgery. Persons of skill will appreciate the ability to extend these concepts to other conditions or fields of medicine. It should be noted that while the present disclosure describes examples in the context of neurosurgery, the present disclosure may be applicable to other procedures that may benefit from fabrication of artificial bone, particularly where such fabrication takes place intraoperative^ or nearly real-time during (e.g., in parallel with) surgery. [0020] Various example apparatuses or processes will be described below. No example embodiment described below limits any claimed embodiment and any claimed embodiments may cover processes or apparatuses that differ from those examples described below. The claimed embodiments are not limited to apparatuses or processes having all of the features of any one apparatus or process described below or to features common to multiple or all of the apparatuses or processes described below. It is possible that an apparatus or process described below is not an embodiment of any claimed embodiment.

[0021] Furthermore, numerous specific details are set forth in order to provide a thorough understanding of the disclosure. However, it will be understood by those of ordinary skill in the art that the embodiments described herein may be practiced without these specific details. In other instances, well-known methods, procedures and components have not been described in detail so as not to obscure the embodiments described herein .

[0022] FIG. 1 illustrates a perspective view of an example minimally invasive port-based surgical procedure. As shown in FIG. 1, a surgeon 101 may conduct a minimally invasive port-based surgery on a patient 102 in an operating room (OR) environment. A craniotomy may be performed as part of the minimally invasive surgery, to provide access to the patient's brain. A localization or navigation system 200 (described further below) may be used to assist the surgeon 101 during the procedure. Optionally, an operator 103 may be present to operate, control and provide assistance with the navigation system 200.

[0023] FIG. 2A shows a diagram illustrating components of an example medical navigation system 200. The disclosed methods and systems for determining dimensions for fabrication of an artificial bone flap may be implemented in the context of the medical navigation system 200. The medical navigation system 200 may include one or more displays 205, 211 for displaying a video image, an equipment tower 201, and a mechanical arm 202, which may support an optical scope 204 (which may also be referred to as an external scope). One or more of the displays 205, 211 may include a touch-sensitive display for receiving touch input. The equipment tower 201 may be mounted on a frame (e.g., a rack or cart) and may contain a power supply and a computer or controller that may execute planning software, navigation software and/or other software to manage the mechanical arm 202 and tracked

instruments. In some examples, the equipment tower 201 may be a single tower configuration operating with dual displays 211, 205, however other configurations may also exist (e.g., dual tower, single display, etc.).

Furthermore, the equipment tower 201 may also be configured with a universal power supply (UPS) to provide for emergency power, in addition to a regular AC adapter power supply. [0024] A portion of the patient's anatomy may be held in place by a holder. For example, as shown the patient's head and brain may be held in place by a head holder 217. An access port 206 and associated introducer 210 may be inserted into the head, to provide access to a surgical site in the head. The optical scope 204 may be attached to the mechanical arm 202, and may be used to view down the access port 206 at a sufficient magnification to allow for enhanced visibility down the access port 206. The output of the optical scope 204 may be received by one or more computers or controllers to generate a view that may be depicted on a visual display (e.g., one or more displays 205, 211).

[0025] In some examples, the navigation system 200 may include a tracked pointer 220. The tracked pointer 220, which may include markers 212 to enable tracking by the tracking camera 213, may be used to identify points (e.g., fiducial points or points bordering a craniotomy opening, as discussed below) on a patient. FIG. 2B shows an example use of a tracked pointer 220 to identify points on a patient. As shown, an operator, typically a nurse or the surgeon 101, may use the tracked pointer 220 to identify the location of points on the patient 102, in order to register the location of selected points on the patient 102 in the navigation system 200. It should be noted that a guided robotic system with closed loop control may be used as a proxy for human interaction. Guidance to the robotic system may be provided by any combination of input sources such as image analysis, tracking of objects in the operating room using markers placed on various objects of interest, or any other suitable robotic system guidance techniques.

[0026] Reference is again made to FIG. 2A. Fiducial markers 212 may be connected to the introducer 210 for tracking by the tracking camera 213, which may provide positional information of the introducer 210 from the navigation system 200. In some examples, the fiducial markers 212 may be alternatively or additionally attached to access port 206. In some examples, the tracking camera 213 may be a 3D infrared optical tracking stereo camera similar to one made by Northern Digital Imaging (NDI). In some examples, the tracking system 213 may be an electromagnetic system (not shown), such as a field transmitter that may use one or more receiver coils located on the tool(s) to be tracked. Known profile of the electromagnetic field and known position of receiver coil(s) relative to each other may be used to infer the location of the tracked tool(s) using the induced signals and their phases in each of the receiver coils. Operation and examples of this technology is further explained in Chapter 2 of "Image-Guided Interventions Technology and Application," Peters, T. ; Cleary, K., 2008, ISBN : 978-0-387-72856-7, incorporated herein by reference. Location data of the mechanical arm 202 and/or access port 206 may be determined by the tracking camera 213 by detection of the fiducial markers 212 placed on or otherwise in fixed relation (e.g., in rigid connection) to any of the mechanical arm 202, the access port 206, the introducer 210, the tracked pointer 220 and/or other pointing tools. The fiducial marker(s) 212 may be active or passive markers. The secondary display 205 may provide output of the computed data of the navigation system 200. In some examples, the output provided by the secondary display 205 may include axial, sagittal and coronal views of patient anatomy as part of a multi-view output.

[0027] The active or passive fiducial markers 212 may be placed on tools (e.g., the access port 206 and/or the optical scope 204) to be tracked, to determine the location and orientation of these tools using the tracking camera and navigation system. The markers 212 may be captured by a stereo camera of the tracking system to give identifiable points for tracking the tools. A tracked tool may be defined by a grouping of markers 212, which may define a rigid body to the tracking system. This may in turn be used to determine the position and/or orientation in 3D of a tracked tool in a virtual space. The position and orientation of the tracked tool in 3D may be tracked in six degrees of freedom (e.g., x, y, z coordinates and pitch, yaw, roll rotations), in five degrees of freedom (e.g ., x, y, z, coordinate and two degrees of free rotation), but preferably tracked in at least three degrees of freedom (e.g., tracking the position of the tip of a tool in at least x, y, z coordinates). In typical use with navigation systems, at least three markers 212 are provided on a tracked tool to define the tool in virtual space, however it is known to be advantageous for four or more markers 212 to be used.

[0028] Camera images capturing the markers 212 may be logged and tracked, by, for example, a closed circuit television (CCTV) camera. The markers 212 may be selected to enable or assist in segmentation in the captured images. For example, infrared (IR)-reflecting markers and an IR light source from the direction of the camera may be used. An example of such an apparatus may be tracking devices such as the Polaris® system available from Northern Digital Inc. In some examples, the spatial position of the tracked tool and/or the actual and desired position of the mechanical arm 202 may be determined by optical detection using a camera. The optical detection may be done using an optical camera, rendering the markers 212 optically visible.

[0029] In some examples, the markers 212 (e.g., reflectospheres) may be used in combination with a suitable tracking system, to determine the spatial positioning position of the tracked tools within the operating theatre. Different tools and/or targets may be provided with respect to sets of markers 212 in different configurations. Differentiation of the different tools and/or targets and their corresponding virtual volumes may be possible based on the specification configuration and/or orientation of the different sets of markers 212 relative to one another, enabling each such tool and/or target to have a distinct individual identity within the navigation system 200. The individual identifiers may provide information to the system, such as information relating to the size and/or shape of the tool within the system. The identifier may also provide additional information such as the tool's central point or the tool's central axis, among other information . The virtual tool may also be determinable from a database of tools stored in or provided to the navigation system 200. The markers 212 may be tracked relative to a reference point or reference object in the operating room, such as the patient 102. [0030] Various types of markers may be used. The markers 212 may all be the same type or may include a combination of two or more different types. Possible types of markers that could be used may include reflective markers, radiofrequency (RF) markers, electromagnetic (EM) markers, pulsed or un-pulsed light-emitting diode (LED) markers, glass markers, reflective adhesives, or reflective unique structures or patterns, among others. RF and EM markers may have specific signatures for the specific tools they may be attached to. Reflective adhesives, structures and patterns, glass markers, and LED markers may be detectable using optical detectors, while RF and EM markers may be detectable using antennas. Different marker types may be selected to suit different operating conditions. For example, using EM and RF markers may enable tracking of tools without requiring a line-of-sight from a tracking camera to the markers 212, and using an optical tracking system may avoid additional noise from electrical emission and detection systems.

[0031] In some examples, the markers 212 may include printed or 3D designs that may be used for detection by an auxiliary camera, such as a wide-field camera (not shown) and/or the optical scope 204. Printed markers may also be used as a calibration pattern, for example to provide distance information (e.g., 3D distance information) to an optical detector. Printed identification markers may include designs such as concentric circles with different ring spacing and/or different types of bar codes, among other designs. In some examples, in addition to or in place of using markers 212, the contours of known objects (e.g., the side of the access port 206) could be captured by and identified using optical imaging devices and the tracking system. [0032] In some examples, the navigation system 200 may include a portable three-dimensional (3D) scanner 222. The 3D scanner 222 may be used to obtain a 3D image of a portion of the patient's anatomy, for example an opening in the skull, as described further below. The image obtained by the 3D scanner 222 may be registered in the virtual space of the navigation system 200, for example by identifying and registering fiducial markers 212 captured in the 3D image. [0033] Minimally invasive brain surgery using an access port 206 is a method of performing surgery on brain tumors. In order to introduce an access port 206 into the brain, the introducer 210, having an atraumatic tip, may be positioned within the access port 206 and employed to position the access port 206 within the patient's brain. The introducer 210 may include fiducial markers 212 for tracking position and orientation of the introducer 210. The fiducial markers 212 may be passive (e.g., reflective spheres for use with an optical tracking system, or pick-up coils for use with an electromagnetic tracking system). The fiducial markers 212 may be detected by the tracking camera 213 and the respective positions of the tracked tool may be inferred by tracking software executed by a computer or controller in connection with the navigation system 200.

[0034] Once the access port 206 has been positioned into the brain, the associated introducer 210 may be removed to allow for access to the surgical site of interest, through the central opening of the access port 206. Tracking of the access port 206 may be provided by an access port guide or by attaching markers to the access port 206 itself.

[0035] A guide clamp 218 (or more generally a guide) for holding the access port 206 may be provided. The guide clamp 218 may allow the access port 206 to be held at a fixed position and orientation while freeing up the surgeon's hands. An articulated arm 219 may be provided to hold the guide clamp 218. The articulated arm 219 may have up to six degrees of freedom to position the guide clamp 218. The articulated arm 219 may be lockable to fix its position and orientation, once a desired position is achieved. The articulated arm 219 may be attached or attachable to a point based on the patient head holder 217, or another suitable point (e.g ., on another patient support, such as on the surgical bed), to ensure that when locked in place, the guide clamp 218 does not move relative to the patient's head.

[0036] In a surgical operating room (or theatre), setup of a navigation system may be relatively complicated; there may be many pieces of equipment associated with the surgical procedure, as well as elements of the navigation system 200. Further, setup time typically increases as more equipment is added. To assist in addressing this, the navigation system 200 may include two additional wide-field cameras to enable video overlay information . One wide-field camera may be mounted on the optical scope 204, and a second wide-field camera may be mounted on the tracking camera 213. Video overlay information can then be inserted into displayed images, such as images displayed on one or more of the displays 205, 211. The overlay information may illustrate the physical space where accuracy of the 3D tracking system (which is typically part of the navigation system) is greater, may illustrate the available range of motion of the mechanical arm 202 and/or the optical scope 204, and/or may help to guide head and/or patient positioning.

[0037] The navigation system 200 may provide tools to the neurosurgeon that may help to provide more relevant information to the surgeon, and may assist in improving performance and accuracy of port- based neurosurgical operations. Although described in the present disclosure in the context of port-based neurosurgery (e.g ., for removal of brain tumors and/or for treatment of intracranial hemorrhages (ICH)), the navigation system 200 may also be suitable for one or more of: brain biopsy, functional/deep-brain stimulation, catheter/shunt placement (in the brain or elsewhere), open craniotomies, and/or endonasal/skull- based/ear-nose-throat (ENT) procedures, among others. The same navigation system 200 may be used for carrying out any or all of these procedures, with or without modification as appropriate.

[0038] For example, although the present disclosure may discuss the navigation system 200 in the context of neurosurgery, the same navigation system 200 may be used to carry out a diagnostic procedure, such as brain biopsy. A brain biopsy may involve the insertion of a thin needle into a patient's brain for purposes of removing a sample of brain tissue. The brain tissue may be subsequently assessed by a pathologist to determine if it is cancerous, for example. Brain biopsy procedures may be conducted with or without a stereotactic frame. Both types of procedures may be performed using image-guidance. Frameless biopsies, in particular, may be conducted using the navigation system 200. [0039] In some examples, the tracking camera 213 may be part of any suitable tracking system. In some examples, the tracking camera 213 (and any associated tracking system that uses the tracking camera 213) may be replaced with any suitable tracking system which may or may not use camera-based tracking techniques. For example, a tracking system that does not use the tracking camera 213, such as a radiofrequency tracking system, may be used with the navigation system 200.

[0040] FIG. 3A is a flow chart illustrating an example method 300 of performing a port-based surgical procedure using a navigation system, such as the medical navigation system 200 described above. At 302, the port-based surgical plan may be imported. A detailed description of an example process to create and select a surgical plan is outlined in PCT application no. PCT/CA2014/050272, titled "PLANNING, NAVIGATION AND SIMULATION SYSTEMS AND METHODS FOR MINIMALLY INVASIVE THERAPY", which claims priority from U .S. provisional patent application nos. 61/800, 155 and 61/924,993. The entireties of all these disclosures are incorporated herein by reference.

[0041] An example surgical plan may include pre-operative 3D imaging data (e.g., magnetic resonance imaging (MRI), computer tomography (CT), positron emission tomography (PET) or ultrasound data). The plan may include overlaid data, such as additional received inputs (e.g., sulci entry points, target locations, surgical outcome criteria and/or additional 3D image data information). The plan may also include a display of one or more planned trajectory paths (e.g., based on calculated score for a projected surgical path). Other surgical plans and/or methods may additionally or alternatively be used as inputs into the navigation system. [0042] Once the plan has been imported into the navigation system at the block 302, the patient may be affixed into position (e.g., using a body holding mechanism, such as the head holder 217). The patient's head position may be also confirmed with the plan using appropriate navigation software (at 304), which in an example may be implemented by the computer or controller forming part of the equipment tower 201.

[0043] Next, registration of the patient may be initiated (at 306). The term "registration" may refer to the process of transforming different sets of data into one coordinate system. Data may include multiple photographs, data from different sensors, times, depths, or viewpoints, for example. The process of registration may be used in the context of the present disclosure for medical imaging, in which images from different imaging modalities may be co-registered. Registration may be used in order to be able to compare and/or integrate the data obtained from these different modalities.

[0044] Registration of the patient to a base reference frame may occur in various suitable ways. Example methods for registration may include:

[0045] Identification of features (natural or engineered) in the image data (e.g ., MR and CT images) and indication of those same features on the actual patient using the tracked pointer 220;

[0046] Tracing a line on the curved profile of the patient's face or forehead with a pointer tool that may be tracked by the tracking camera, and matching this curved profile to the image data (e.g., 3D MR or CT volume);

[0047] Application of a tool of known geometry to the patient's face, where the tool may have targets tracked by the tracking camera; or

[0048] Using a surface acquisition tool, such as the 3D scanner 222 (which may operate based on structured light), to extract a surface of the patient's face or forehead and matching the extracted surface to the 3D clin ical image data (e.g., 3D MR or CT volume) that is acquired prior to or during the surgical procedure. The matching process may also be known as registration or image fusion . The process may involve, for example, aligning common features, such as anatomical structures, in images acquired using different modalities by transforming one image relative to the other. The resulting geometric transformation provides a means of correlating points in clinical images to coordinate frame of the operating room. Hence, the navigation system 200 can help a surgeon visualize the positions of physical surgical tools relative to clinical images, such as MR, CT and ultrasound.

[0049] Various registration techniques available to those skilled in the art may be suitable, and one or more of these techniques may be applied to the present disclosure. Non-limiting examples include intensity- based methods that compare intensity patterns in images via correlation metrics, as well as feature-based methods that find correspondence between image features such as points, lines, and contours, among other possible methods. Image registration methods may also be classified according to the transformation models they use to relate the target image space to the reference image space. Another classification can be made between single-modality and multi-modality methods. Single- modality methods typically register images in the same modality acquired by the same scanner or sensor type, for example, a series of MR images may be co-registered, while multi-modality registration methods are used to register images acquired by different scanner or sensor types, for example in MRI and PET. In the present disclosure, multi-modality registration methods may be used in medical imaging of the head and/or brain as images of a patient are frequently obtained from different scanners. Examples include registration of brain CT/MRI images or PET/CT images for tumor localization, registration of contrast-enhanced CT images against non-contrast-enhanced CT images, and registration of ultrasound and CT. [0050] FIG. 3B shows a flow chart illustrating example methods that may be used to carry out the registration of the block 306. Block 340 illustrates an approach using fiducial touch points, while block 350 illustrates an approach using a surface scan. The block 350 is not typically used when fiducial touch points or a fiducial pointer is used.

[0051] If the use of fiducial touch points (at 340) is contemplated, the method may involve first identifying fiducial points on images (at 342), then touching the corresponding touch points on the patient with the tracked pointer 220 (at 344). Next, the navigation system may compute the registration to reference markers (at 346).

[0052] If a surface scan procedure (at 350) is used, the patient's head (e.g., face, back of head and/or skull) may be scanned using the 3D scanner 222 (at 352). Next, the corresponding surface of the patient's head may be extracted from image data (e.g ., MR or CT data) (at 354). Finally, the scanned surface and the extracted surface may be matched to each other to determine registration data points (at 356).

[0053] Upon completion of either the fiducial touch points (at 340) or surface scan (at 350) procedures, the data extracted may be computed and used to confirm registration at block 308, shown in FIG. 3A. [0054] Referring back to FIG. 3A, once registration is confirmed (at 308), the patient may be draped (at 310). Typically, draping involves covering the patient and surrounding areas with a sterile barrier to create and maintain a sterile field during the surgical procedure. Draping may be used to eliminate the passage of microorganisms (e.g., bacteria) between non-sterile and sterile areas.

[0055] Upon completion of draping (at 310), the patient

engagement points may be confirmed (at 312) and then the craniotomy may be prepared and planned (at 314). [0056] Upon completion of the preparation and planning of the craniotomy (at 314), the craniotomy may be cut and a bone flap may be removed from the skull to access the brain (at 316). In some examples, cutting the craniotomy may be assisted by a visual indication of the location, size and/or shape of the planned craniotomy (e.g ., a projection of a planned outline onto the patient's sku ll) . Registration data may be updated with the navigation system at this point (at 322).

[0057] Next, the engagement within craniotomy and the motion range may be confirmed (at 318). Next, the procedure may advance to cutting the dura at the engagement points and identifying the sulcus (at 320). Registration data may again be updated with the navigation system at this point (at 322).

[0058] In some examples, by focusing the camera's view on the surgical area of interest, update of the registration data (at 322) may be adjusted to help achieve a better match for the region of interest, while ignoring any non-uniform tissue deformation, for example, affecting areas outside of the region of interest. Additionally, by matching image overlay representations of tissue with an actual view of the tissue of interest, the particular tissue representation may be matched to the live video image, which may help to improve registration of the tissue of interest. For example, the registration may enable: matching a live video of the post craniotomy brain (with the brain exposed) with an imaged sulcal map; matching the position of exposed vessels in a live video with image segmentation of vessels; matching the position of lesion or tumor in a live video with image segmentation of the lesion and/or tumor; and/or matching a video image from endoscopy up the nasal cavity with bone rendering of bone surface on nasal cavity for endonasal alignment.

[0059] In some examples, multiple cameras can be used and overlaid with tracked instrument(s) views, which may allow multiple views of the image data and overlays to be presented at the same time. This may help to provide greater confidence in registration, or may enable easier detection of registration errors and their subsequent correction.

[0060] Thereafter, the cannulation process may be initiated .

Cannulation typically involves inserting an access port into the brain, typically along a sulcus path as identified at 320, along a trajectory plan . Cannulation is typically an iterative process that may involve repeating the steps of aligning the port on engagement and setting the planned trajectory (at 332) and then cannulating to the target depth (at 334) until the complete trajectory plan is executed (at 324).

[0061] In some examples, the cannulation process may also support multi-point trajectories where a target (e.g., a tumor) may be accessed by cannulating to intermediate points, then adjusting the cannulation angle to get to the next point in a planned trajectory. This multi-point trajectory may be contrasted with straight-line trajectories where the target may be accessed by cannulating along a straight path directly towards the target. The multi-point trajectory may allow a cannulation trajectory to skirt around tissue that the surgeon may want to preserve. Navigating multipoint trajectories may be accomplished by physically reorienting (e.g., adjusting the angle of) a straight access port at different points along a planned path, or by using a flexible port, such as an access port with manipulatable bends that may be bent along the multi-point trajectory. In some examples, the skull opening created by the craniotomy at 316 may be widened by cutting out more bone during the cannulation process. Widening of the sku ll opening may be needed to achieve the desired cannulation angle, for example, where the original craniotomy was found to be insufficient.

[0062] Once cannulation of the access port is complete, the surgeon may perform resection (at 326) to remove part of the brain and/or tumor of interest, with or without having first removed the introducer (if used). The surgeon may then decannulate (at 328) by removing the port from the brain. Finally, the surgeon may close the dura and complete the craniotomy (at 330). Closure of the craniotomy may involve replacement of the bone flap removed at 316, or may involve closure using an artificial bone flap, which may be fabricated intra-operatively as described further below. Some aspects of FIGS. 3A and 3B may be specific to port-based surgery, such as portions of blocks 328, 320, and 334. Appropriate portions of these blocks may be skipped or suitably modified when performing non-port-based surgery.

[0063] FIG. 4 shows an example of how, during use, the navigation system 200 may be operated to determine a coordinate frame 440, which contains the actual spatial locations of tracked elements (e.g ., the mechanical arm 202, the access port 206, the introducer 210, the tracked pointer 220 and/or other pointing tools) in the operating room and their spatial relations to one another. Another example of such tracked elements may be a surgical real-time imaging camera such as the optical scope 204. This may be a moveable camera used for visualization of the surgical area of interest, a surgical volume of interest such as a brain, and/or medical instruments. A 3D virtual volume representing preoperative image data of patient anatomy (e.g., obtained prior to the procedure using suitable imaging modalities such as MR or CT) may be provided to the navigation system 200, and may be displayed on one or more displays 205, 211. In some examples, the virtual volume may be acquired using a patient with attached fiducial markers (not shown). The fiducial markers may remain attached in place on the patient (or else their locations may have been marked on the patient) in a manner which persists through the registration step in order to register the pre-operative imaging data with the patient in the operating room.

[0064] For example, actual fiducial markers positioned on the patient's head may be virtually in the same position relative to the patient's virtual brain scan as the actual fiducial markers relative to the patient's actual brain. The spatial correspondence between the actual fiducial markers and the virtual fiducial markers permits the actual and virtual coordinate frames to be aligned, which allows for an accurate overlay of virtual image data onto the actual image data . [0065] This overlay of images may be achieved by combining video from a virtual camera 410 depicting the virtual operating room (OR) surgical field and video from an actual surgical imaging camera 420 depicting the actual OR surgical field. To obtain an accurate overlay, the two cameras 410, 420 should be coincidentally aligned and have substantially the same optical properties. Hence the alignment of the virtual camera 410 in a virtual coordinate frame 430 (defined in the navigation system 200) may be constrained to be equivalent to the alignment of the actual camera 420, relative to the actual coordinate frame 440 of the operating room, and have the same optical properties as the actual camera 420, namely, the same field-of-view, aspect ratio, and optical distance. This may be accomplished using the navigation system 200. Given an initial d iscrepancy or spatial separation 415 between the coordinate frames 430, 440, the tracked pointer 220 controlled by a user 450 (e.g., a surgeon 101) may be used to confirm the spatial location of the actual fiducial markers in virtual space as depicted in a picture frame 480 shown in the upper right hand side in FIG. 4.

[0066] In general, each time a point is identified, the virtual and actual coordinate frames 430, 440 become more accurately aligned. For example, as the tip of the tracked pointer 220 indicates the spatial position of a fiducial marker in actual space (in this example, located above the left eyebrow of the patient), its virtual counterpart fiducial marker aligns with it resulting in the navigation system virtual coordinate frame 430 to transform 460 and align its origin with the operating room actual coordinate frame 440. This also results in the two cameras 410,

420 realigning themselves accordingly. It should be noted that the relative shift in alignment of the cameras 410, 420, an example of which is shown between diagrams 490 and 400, may be proportional to the shift between the virtual alignment of the overlay on the actual image data between diagrams 490 and 400.

[0067] In some examples, the coordinate frames 430, 440 may be still rotationally misaligned, as illustrated in the example bottom left picture frame 400 in FIG. 4. Accordingly, the alignment process may be repeated and another point is registered. In this example iteration the fiducial marker being aligned is located near the right ear of the patient and this causes a rotation of the virtual coordinate frame 430, resulting in it and the actual coordinate frame 440 to better coincidently align.

[0068] Repetition of the above steps results in the production of a common coordinate frame, and accurate registration, as can be seen in diagram 405 (in the lower right hand side of FIG. 4) which shows the accurate overlay of the virtual and actual brain as a result of the coincident alignment of the virtual and actual cameras 410, 420, respectively.

[0069] FIG. 5 shows a block diagram of an example system configuration that may be used to carry out the functions of a navigation system, as disclosed herein. The example system may include a control and processing unit 500 and other external components.

[0070] In some examples, the control and processing unit 500 may include one or more processors 502 (for example, a CPU and/or microprocessor), one or more memories 504 (which may include random access memory (RAM) and/or read-only memory (ROM)), a system bus 506, one or more input/output interfaces 508 (such as a user interface for a user (e.g., a clinician or a surgeon) to provide various inputs (e.g., to perform trajectory planning or run simulations)), one or more

communications interfaces 510, and one or more internal storage devices 512 (e.g. a hard disk drive, compact disk drive and/or internal flash memory). The control and processing unit may also include a power supply (not shown).

[0071] The control and processing unit 500 may interface with one or more other external devices, such as a tracking system or navigation system (e.g ., the navigation system 200 of FIG. 2), a data storage device 542, and external input and/or output devices 544 which may include, for example, one or more of a display, keyboard, mouse, foot pedal, microphone and speaker. The data storage device 542 may include any one or more suitable data storage devices, such as a local or remote computing device (e.g., a computer, a hard drive, a digital media device, or a server) which may have a database stored thereon. In the example shown in FIG. 5, the data storage device 542 may store identification data 550 for identifying one or more medical instruments 560 and configuration data 552 that may associate customized configuration parameters with the one or more medical instruments 560. The data storage device 542 may also store preoperative image data 554 and/or medical procedure planning data 556. Although the data storage device 542 is shown as a single device, the data storage device 542 may be provided as one or more storage devices.

[0072] The medical instrument(s) 560 may be identifiable by the control and processing unit 500. The medical instrument(s) 560 may be connected to, and controlled by, the control and processing unit 500, or may be operated or otherwise employed independently of the control and processing unit 500. The navigation system 200 may be employed to track one or more of the medical instrument(s) 560 and spatially register the one or more tracked medical instruments 560 to an intraoperative reference frame, for example as discussed above.

[0073] The control and processing unit 500 may also interface with one or more other configurable devices 520, and may intraoperatively reconfigure one or more of such device(s) 520 based on configuration parameters obtained from configuration data 552, for example. Examples of the device(s) 520 may include one or more external imaging devices 522, one or more illumination devices 524, the mechanical arm 202, one or more projection devices 528, and one or more displays 205, 211.

[0074] Various embodiments and aspects of the present disclosure may be implemented via the processor(s) 502 and/or memory(ies) 504. For example, one or more of the functionalities and methods described herein may be at least partially implemented via hardware logic in the processor(s) 502 and/or at least partially using instructions stored in the memory(ies) 504, as one or more processing engines 570 (also referred to as modules). Example processing engines 570 include, but are not limited to, a user interface engine 572, a tracking engine 574, a motor controller 576, an image processing engine 578, an image registration engine 580, a procedure planning engine 582, a navigation engine 584, and a context analysis engine 586. Although certain engines (or modules) are described, it should be understood that engines or modules need not be specifically defined in the instructions, and an engine or module may be used to implement any combination of functions.

[0075] It is to be understood that the system is not intended to be limited to the components shown in FIG. 5. For example, one or more components of the control and processing unit 500 may be provided as an external component or device. Although only one of each component is illustrated in FIG. 5, any number of each component can be included . For example, a computer typically contains a number of different data storage media . Furthermore, although the bus 506 is depicted as a single connection between all of the components, the bus 506 may represent one or more circuits, devices or communication channels which link two or more of the components. For example, in personal computers, the bus 506 may include or may be a motherboard.

[0076] In some examples, the navigation engine 584 may be provided as an external navigation system that may interface with or be integrated with the control and processing unit 500.

[0077] Some embodiments or aspects of the present disclosure may be implemented using the processor 502 without additional instructions stored in the memory 504. Some embodiments or aspects of the present disclosure may be implemented using instructions stored in the memory 504 for execution by one or more general purpose microprocessors. In some examples, the control and processing unit 500 (which may be also referred to as a computer control system) may be, or may include, a general purpose computer or any other hardware equivalents configured for operation in space. The control and processing unit 500 may also be implemented as one or more physical devices that may be coupled to the processor(s) 502 through one or more communications channels or interfaces. For example, the control and processing unit 500 may be implemented using application specific integrated circuits (ASIC). In some examples, the control and processing unit 500 may be implemented as a combination of hardware and software, such as where the software may be loaded into the processor(s) 502 from the memory(ies) 504 or internal storage(s) 512, or from an external source (e.g., via the communication interface(s) 510, such as over a network connection). Thus, the present disclosure is not limited to a specific configuration of hardware and/or software. [0078] FIG. 6 illustrates the tissues that may be encountered during the port-based surgery. As illustrated, the tissues may include a skull 600, a dural layer 610 (or dura), a cerebrospinal fluid (CSF) layer 620, blood vessels 630, and a brain section including grey matter 640, white matter 650, diffusion or brain fibers 660, and a tumor target 670. [0079] FIG. 7A is a flow chart outlining an example method 700 for fabricating an artificial bone flap. FIG. 7B shows further details of the method 700. The method 700 may be carried out within the context of the navigation system 200, as described above. Although the surgeon 101 is described as being the principle operator in the method 700, a nurse or other operator 103 may alternatively or additionally be involved in carrying out the method.

[0080] At 710, a reference image of at least a portion of the patient's skull may be obtained. The reference image may be a preoperative image or may be obtained during the procedure (but prior to performing the craniotomy). The reference image is typically a 3D image, which may be obtained using a MR or CT imaging system, or the 3D scanner 222. The reference image may be obtained using suitable techniques to image the patient's bone. For example, an appropriate pulse sequence may be selected for MR image acquisition, in order to capture bone tissue. In some examples, ultrashort echo time (UTE) MRI methods may be used to image the patient's bone. Where the reference image is a MR or CT image, the reference image may be obtained pre-operatively, for example prior to the process illustrated in FIG. 3A, and the reference image may additionally be used for planning the procedure. In the case of a 3D surface scan using the 3D scanner 222, the reference image may be obtained after the patient has been prepped (e.g., after the patient's hair has been shaved in the required region or after the skull has been exposed) but before performing the craniotomy. The reference image may be used to capture the shape of the skull bone prior to craniotomy.

[0081] The reference image may capture one or more fiducial markers positioned at relatively fixed positions on the patient's head or skull. Such fiducial markers may remain in place during the length of the procedure, to ensure proper registration of virtual and actual coordinate systems, as described above. In some examples, fiducial markers may be placed during on the patient's exposed skull in the vicinity of the planned craniotomy. Fiducial markers placed directly on the exposed skull may be captured by a 3D surface scan using the 3D scanner 222. By placing fiducial markers directly on the exposed skull, unwanted shifting of the fiducial markers due to movement of the patient's skin may be avoided.

[0082] The reference image may be used (at 710 or later in the method 700) to determine the curvature and thickness of the skull at the site of the craniotomy. Where such reference image is lacking in quality or missing, alternative methods, such as those described further below, may be used to infer curvature of the skull at or around the craniotomy location . [0083] The craniotomy may be performed, and at 720 intraoperative data of the craniotomy opening may be obtained. Obtaining the intra-operative data may include obtaining 3D image data 750, obtaining a set of points defining a boundary of the craniotomy 760 and/or obtaining 2D image data 770.

[0084] At 750, obtaining 3D image data of the craniotomy may include obtaining a 3D surface scan of the craniotomy, such as by using a portable 3D scanner 222 or using optical coherence tomography (OCT) imaging (e.g., using a remotely operated robotically guided OCT system). Typically, OCT imaging may allow the imaging of surface structures and sub-surface structures up to a limited depth (e.g., around 3mm), and at a relatively high resolution. A method for obtaining OCT surface images may involve the use of steerable mirrors to scan a beam of light across the surface being imaged; however, the scanned area is often a maximum of 1 cm ² , which is too small to cover the full area of a typical craniotomy. The surface area covered by the OCT scan may be increased by systematically moving the scanning head of the OCT system (e.g., using a robotic system to ensure precise and systematic movement), obtaining individual scans at each position, and then combining the small scanned areas together to form a larger surface map. A surface scan obtained using OCT in this way would also contain information about sub-surface structures up to the limited depth permitted by OCT. The 3D image data may capture the positions of the fiducial markers on the patient, to enable the captured intra-operative data to be related to the reference image obtained at 710. The 3D image data may capture the size, shape and depth of the skull opening created by the craniotomy. [0085] At 760, data defining a boundary of the craniotomy may be obtained as a set of points along the boundary of the craniotomy. For example, the boundary may be defined by the surgeon 101 manually touching points or tracing along the border of the craniotomy directly on the patient's skull using a tracked pointer 220. By tracking and storing a series of positional data of the tip of the tracked pointer 220 during the tracing, a series of points defining the border of the craniotomy may be obtained. While touching or tracing the border of the craniotomy, the positional data of the tip of the tracked pointer 220 may be automatically tracked and stored (e.g., at regular time intervals, such as every 500 ms) by the navigation system 200. Alternatively, the surgeon 101 may manually trigger the storage of positional data at each touched point. [0086] The tracked pointer 220 may also be used to indicate the thickness of the sku ll (e.g., by collecting positional data at points on the outer and inner edges of the craniotomy) and/or may also be used to indicate the curvature of the exposed dura (e.g., by collecting positional data at points on various locations on the dura). In some examples, this data may be used to approximate the thickness and/or curvature of the artificial bone flap to be fabricated .

[0087] In some examples, after a set of points defining the boundary of the craniotomy has been obtained, the surgeon 101 may provide input to the computer or control unit to indicate that the set of data is complete. The computer or control unit may then verify the collected data for consistency and completeness (e.g ., perform algorithms to verify that the boundary forms a closed loop, that the boundary falls within the planned craniotomy and/or that the boundary does not deviate significantly from the planned craniotomy) and may cause the defined boundary to be displayed (e.g ., overlaid on a 2D image on the display 205, 211) for confirmation by the surgeon 101. In some examples, such verification and/or feedback may be provided to the surgeon 101 during the obtaining of the set of points, to inform the surgeon 101 whether more points are needed or whether a sufficient number of points has been obtained.

[0088] At 770, obtaining 2D image data of the craniotomy may include obtaining a 2D optical image or video of the craniotomy, such as using the optical scope 204. The 2D image data may capture the position of the fiducial markers on the patient, to enable the captured intra- operative data to be related to the reference image obtained at 710. [0089] At 772, a boundary of the craniotomy may be determined in the 2D image. For example, the boundary may be determined by manually defining the boundary in a captured 2D image. The 2D image may be displayed on the display 205, 211 and the surgeon 101 may use mouse input or touchscreen input, for example, to draw or trace the boundary of the craniotomy as shown in the 2D image. Alternatively or as an additional verification, the computer or control unit may perform an automatic edge detection algorithm to determine the boundary of the craniotomy as displayed in the 2D image. [0090] In some examples, after the boundary of the craniotomy has been defined in the 2D image, the surgeon 101 may provide input to the computer or control unit to ind icate that the input is complete. The computer or control unit may then verify the data for consistency and completeness (e.g., verify that the boundary forms a closed loop, that the boundary falls within the planned craniotomy and/or that the boundary does not deviate significantly from the planned craniotomy) and may display the defined boundary (e.g., overlaid on the 2D image on the display 205, 211) for confirmation by the surgeon 101.

[0091] In some examples, obtaining intra-operative data of the opening at 720 may include verification that the measured opening matches the planned craniotomy (e.g., as planned at 314 in FIG. 3A). If the intra-operative data indicates a location, size and/or shape of the craniotomy that deviates from the planned craniotomy by more than a predetermined amount (e.g., a difference of more than 1cm) a warning or notification may be generated (e.g., as a visual display on the display 205, 211) indicating that the intra-operative data may be inaccurate or that the craniotomy may differ significantly from the plan.

[0092] At 730, the dimensions of the opening may be calculated based on the reference image and the intra-operative data . Where the intra-operative data has not been registered with the reference image, a registration of the intra-operative data and the reference image may be carried out as part of block 730. The intra-operative data may be compared against the reference image to determine the size, shape, thickness and/or curvature of the bone flap that was removed to create the opening. [0093] Where the intra-operative data includes 3D image data (e.g., as obtained at 750), calculating the dimensions of the opening may include registering the 3D image data to the reference image (at 756) and comparing the 3D image data to the reference image (at 758).

[0094] At 756, registration of the 3D image data to the reference image may include identifying fiducial markers captured in each of the 3D image and the reference image and registering the fiducial markers of each image to each other, using suitable registration techniques.

[0095] At 758, the registered 3D and reference images may then be compared against each other to determine the portion of the skull (in the reference image) that was cut to form the opening (in the 3D image). For example, the 3D image may be subtracted from the reference image in order to obtain the portion of the skull that was cut to form the opening.

[0096] Where the intra-operative data includes a set of points defining a boundary of the opening (e.g., as obtained at 760), calculating the dimensions of the opening may include determining the boundary defined by the set of points (at 764), registering the boundary to the reference image (at 766) and determining the dimensions of the skull (in the reference image) that falls within the boundary (at 768).

[0097] At 764, determining the boundary defined by the set of points may be carried out using suitable algorithms for connecting the points to generate a relatively smooth, closed loop. Example mathematical algorithms for defining such boundary include cubic spline routines and polynomial functions in 3D space. The surface of the skull may be also incorporated using spline surfaces, which are smooth surfaces with defined curvature and boundary. In other words, the spline surface may be a mathematical model of the removed bone flap. This may be carried out using the computer or control unit in the navigation system.

Determining the boundary may include quality assurance checks. For example, the computer or control unit may verify that there are a sufficient number of points to generate a smooth, closed loop, that the boundary falls within the planned craniotomy and/or that the boundary does not deviate significantly from the planned craniotomy. One or more of these quality assurance checks may also be carried out while obtaining the set of points at 760, and feedback may be provided to the surgeon 101 during the obtaining, to indicate whether more points are needed.

[0098] At 766, the determined boundary may be registered to the reference image by relating the location of the set of points to the reference image in the virtual coordinate system . Since the set of points may be obtained using the tracked pointer 222, the location of each point may already be defined in the virtual coordinate system. Using the known virtual coordinates of fiducial markers in the reference image, the determined boundary may be registered to the reference image. In some examples, registration of the set of points to the reference image may take place before determining the boundary. Registering the set of points to the reference image before determining the boundary may be useful for performing quality assurance checks.

[0099] At 768, the dimensions of the skull within the boundary may be determined by determining the dimensions (including skull thickness and curvature, for example) of the reference image that is bounded by the registered boundary.

[00100] Where the intra-operative data includes 2D image data and a boundary determined in the 2D image data (e.g ., as obtained at 770 and 772), calculating the dimensions of the opening may include registering the 2D image data to the reference image (at 776) and determining the dimensions of the skull (in the reference image) that falls within the boundary (at 778).

[00101] At 776, registering the 2D image data to the reference image may include identifying fiducial markers captured in each of the 2D image and the reference image and registering the fiducial markers of each image to each other, using suitable registration techniques. Once the 2D image is registered with the reference image, the boundary determined in the 2D image (at 772) may be automatically registered to the reference image.

[00102] At 778, determining the dimensions of the skull within the boundary may include determining the dimensions (including skull thickness and curvature, for example) of the reference image that is bounded by the registered boundary. Where such reference image is lacking in resolution or missing, it may be augmented by interpolating the intra-operative 3D scan of the intact portion of the skull or head to infer the curvature of the removed bone flap piece. This interpolation may be performed, for example, by creating a mathematical grid to represent the entire head using the intact portion of the head. Then, assuming that the head surface, and hence the skull surface, is relatively smooth, the surface grid may be interpolated over the bone flap region to arrive at a "filled in" model. The latter information may then be used to represent the curvature of the bone flap surface.

[00103] At 740, the calculated dimensions for fabricating the artificial bone flap may be provided. This may include providing data suitable for use by a fabrication system, for fabricating the artificial bone flap. The calculated dimensions may be transmitted to the fabrication system in the form of data signals (e.g., through wired or wireless communication) or may be provided in a tangible form (e.g ., a storage medium such as a computer readable memory) to be manually transferred to the fabrication system. [00104] In some examples, the computer or control unit may carry out further processing of the dimensions before providing the dimensions to a fabrication system. For example, the calculated dimensions of the opening may be provided in the form of a digital 3D model of the artificial bone flap that is to be fabricated. In some examples, the 3D model may be only for a portion of the removed bone flap, such as a remaining portion of the natural bone flap has been preserved. This may be useful where only a portion of the natural bone flap could be salvaged. This approach may help with bone regeneration and patient healing, as part of the living tissue is reused.

[00105] In some examples, the calcu lated dimensions may be used to facilitate selection and/or cutting of a segment of an artificial dura (e.g ., made of a synthetic or biological material) which may be used to close the open dura in the patient. In some examples, the calculated dimensions may help in selection of an artificial dura from a pre-existing inventory of differently-sized artificia l duras. The cutting of a segment of the artificial dura (either cutting the artificial dura from a large piece of material or trimming of a pre-sized piece of material) may be guided by a boundary that is optically projected on to the cutting surface. The projected boundary may be generated based on the calculated dimensions provided at 740. Example techniques for projecting a boundary on the artificial dura include a laser dot that is moved reasonably swiftly over the surface of the artificial dura to generate a cutting track or an image directly projected on the cutting surface using projected light from a fixed distance, for example. [00106] In some examples, the computer or control unit may, in addition to the calculated dimensions, provide scaled versions (e.g ., 95% or 90%) of the calculated dimensions, in order to fabricate one or more artificial bone flaps that are slightly smaller than the actual calculated dimensions of the craniotomy. Fabricating the artificial bone flap to be slightly smaller than the calculated dimensions of the opening may be useful to provide a margin of error (e.g ., to accommodate possible errors in determining the boundary of the craniotomy) when fitting the artificial bone flap into the opening. A slightly smaller artificial bone flap may also provide a small gap between the perimeter of the artificial bone flap and the patient's skull, into which bonding substances and devices (e.g., bio- adhesives, sutures, plates and/or wires) may be introduced to aid in healing.

[00107] The calculated dimensions may be provided (e.g., as a digital model) as input to a fabrication system for additive or subtractive 3D manufacturing. Any suitable rapid prototyping system may be used to fabricate the artificial bone flap. Additive 3D manufacturing may also be referred to as 3D printing and may include various suitable manufacturing techniques including extrusion deposition, binding of granular materials, laminated object manufacturing, or photopolymerization, among others. Subtractive 3D manufacturing may include techniques such as etching, cutting or drilling, among others. The fabrication of the artificial bone flap may be relatively fast (e.g ., being complete in time for the artificial bone flap to be used to close the craniotomy at the end of the procedure), such as within less than 30 minutes. Where the fabrication technique is suitably fast, multiple artificial bone flaps may be manufactured while the procedure is still ongoing. [00108] The calculated dimensions may be also used to facilitate selection of an artificial bone flap from a pre-existing inventory of differently-sized artificia l bone flaps. For example, artificial bone flap replacement components may be purchased in different predefined sizes. The calculated dimensions may aid in selecting the desired predefined size that meets the needs of a particular procedure. Further, after the artificial bone flap has been selected from predefined sizes, the calculated dimensions may be further used to trim the pre-sized artificial bone flap to meet the exact dimensional requirements for the procedure. In some examples, the fabricated artificial bone flap may be used to help shape (e.g ., bend) other materials that will also be used to close the cranial opening. For example, the artificia l bone fla p may serve as a guide to help bend mesh-like cranial opening covers so that the mesh structures closely match the curvature that is present on the head surface in the vicinity of the cranial opening .

[00109] The artificial bone flap may be fabricated using any suitable biocompatible material. In some examples, the artificial bone flap may be fabricated to be relatively porous, to assist in bone growth and patient healing. Examples of suitable materials include calcium phosphate, polyethylene, bioactive glass and demineralized bone. Other materials may be used. Details of the suitability of va rious materials are presented in "Reconstruction of Skull Defects: Currently Available Materials," Goiato et.al., J Craniofac Surg 2009; 20 : 1512 - 1518, which is hereby

incorporated by reference.

[00110] In some examples, more than one artificial bone flap may be fabricated. The plurality of artificial bone flaps may be identical or may be different in material and/or dimensions. For example, different artificial bone flaps may be fabricated using different materials (e.g., selected among a variety of suitable biocompatible materials), which may be useful to enable the surgeon to select the artificial bone flap having a desired material property (e.g., stiffness) to suit the patient. Different artificial bone flaps may also be fabricated with different dimensions. For example, several artificial bone flaps may be fabricated at 100%, 90% and 80% of the size of the calculated dimensions. By providing a variety of sizes, the surgeon may be able to select the artificial bone flap that accommodates a desired bonding method and/or best fits the actual craniotomy opening. The fit of a fabricated artificial bone flap may be assessed by holding the artificial bone flap in the field of view of the camera system used at 770. The image processing system used to estimate the profile and dimensions of the craniotomy may be used to estimate similar information for the artificial bone flap. The computed profile and dimensions of the artificial bone flap may be then automatically compared to those of the craniotomy to confirm that the artificial bone flap will fit the craniotomy opening without having to actually place the fabricated bone flap on the opening. [00111] The artificial bone flap may then be used to close the craniotomy, using suitable techniques, instead of the original bone flap removed to create the craniotomy.

[00112] The present disclosure enables an artificial bone flap to be fabricated while a neurosurgery is ongoing. The measurement, fabrication and completion of the artificial bone flap may all take place during the procedure, and in near real-time, in parallel with the procedure. Thus, the artificial bone flap can be customized to the specific craniotomy created and be available to close the craniotomy at the end of the procedure. [00113] Obtaining a reference image (e.g., a MR or CT image) of the patient's skull is typically already performed as part of pre-operative planning, and obtaining intra-operative data of the craniotomy opening may be relatively simple and quick (e.g., obtaining a 3D image using a portable 3D scanner). Thus, the present disclosure may be implementable in standard neurosurgery with relatively little impact on the length and/or complexity of the procedure.

[00114] In some examples, the present disclosure may be used to create an artificial bone flap to close a skull opening for a patient on whom a craniectomy was previously performed . This may be useful for cases where the original bone flap may be no longer available or where preserving the original bone flap for an extended period of time may be problematic. In some examples, larger portions of the skull may be artificially fabricated for the purpose of maxiofacial reconstruction. The present disclosure may also be adapted to fabricate vertebral components or bodies for the purpose of reconstructive surgery of the spine.

[00115] In some examples, the present disclosure may be

implemented in addition to or as a backup for conventional procedures that use the patient's original bone flap to close the craniotomy. For example, the artificial bone flap may be fabricated as a backup in case the original bone flap is or becomes unsuitable for closing the craniotomy (e.g ., the original bone flap is or becomes damaged or contaminated). Though the present disclosure provides examples in the context of cranial surgery, the disclosed systems and methods may be applied to any other suitable procedure where a portion of the bone or rigid anatomical structure needs to be removed during a surgical procedure and then replaced at the conclusion of the procedure. Examples of such procedures include maxiofacial procedures and spinal procedures where portion of the spinal structure may be removed for subsequent replacement with real or artificial bone structure. [00116] While some embodiments or aspects of the present disclosure may be implemented in fully functioning computers and computer systems, other embodiments or aspects may be capable of being distributed as a computing product in a variety of forms and may be capable of being applied regardless of the particular type of machine or computer readable media used to actually effect the distribution.

[00117] At least some aspects disclosed may be embodied, at least in part, in software. That is, some disclosed techniques and methods may be carried out in a computer system or other data processing system in response to its processor, such as a microprocessor, executing sequences of instructions contained in a memory, such as ROM, volatile RAM, nonvolatile memory, cache or a remote storage device.

[00118] A computer readable storage medium may be used to store software and data which when executed by a data processing system causes the system to perform various methods or techniques of the present disclosure. The executable software and data may be stored in various places including for example ROM, volatile RAM, non-volatile memory and/or cache. Portions of this software and/or data may be stored in any one of these storage devices.

[00119] Examples of computer-readable storage media may include, but are not limited to, recordable and non-recordable type media such as volatile and non-volatile memory devices, read only memory (ROM), random access memory (RAM), flash memory devices, floppy and other removable disks, magnetic disk storage media, optical storage media (e.g ., compact discs (CDs), digital versatile disks (DVDs), etc.), among others. The instructions can be embodied in digital and analog

communication links for electrical, optical, acoustical or other forms of propagated signals, such as carrier waves, infrared signals, digital signals, and the like. The storage medium may be the internet cloud, or a computer readable storage medium such as a disc.

[00120] Furthermore, at least some of the methods described herein may be capable of being distributed in a computer program product comprising a computer readable medium that bears computer usable instructions for execution by one or more processors, to perform aspects of the methods described. The medium may be provided in various forms such as, but not limited to, one or more diskettes, compact disks, tapes, chips, USB keys, external hard drives, wire-line transmissions, satellite transmissions, internet transmissions or downloads, magnetic and electronic storage media, digital and analog signals, and the like. The computer useable instructions may also be in various forms, including compiled and non-compiled code.

[00121] At least some of the elements of the systems described herein may be implemented by software, or a combination of software and hardware. Elements of the system that are implemented via software may be written in a high-level procedural language such as object oriented programming or a scripting language. Accordingly, the program code may be written in C, C+ + , J + +, or any other suitable programming language and may comprise modules or classes, as is known to those skilled in object oriented programming. At least some of the elements of the system that are implemented via software may be written in assembly language, machine language or firmware as needed. In either case, the program code can be stored on storage media or on a computer readable medium that is readable by a general or special purpose programmable computing device having a processor, an operating system and the associated hardware and software that is necessary to implement the functionality of at least one of the embodiments described herein . The program code, when read by the computing device, configures the computing device to operate in a new, specific and predefined manner in order to perform at least one of the methods described herein.

[00122] While the teachings described herein are in conjunction with various embodiments for illustrative purposes, it is not intended that the teachings be limited to such embodiments. On the contrary, the teachings described and illustrated herein encompass various alternatives, modifications, and equivalents, without departing from the described embodiments, the general scope of which is defined in the appended claims. Except to the extent necessary or inherent in the processes themselves, no particular order to steps or stages of methods or processes described in this disclosure is intended or implied. In many cases the order of process steps may be varied without changing the purpose, effect, or import of the methods described.