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  2. Top Orbital and Skull 3D Model STL Files on embodi3D® In our day-to-day lives, we rely on vision more than any of the other four senses, so it only makes sense that human anatomy has adapted to include several features which keep our eyes safe: tear ducts, eyelids, and of course the orbital bone. The orbit (also known as the "eye socket") provides a rigid form of support and protection for some of the most sensitive parts of the eye including the central retinal artery, maeula, retina, choroid, and sclera. The orbit has such complex anatomical features that modeling can prove difficult, and in many instances, the finer features of the orbital bone have been simply been averaged out. The orbital structure isn't one bone, but seven: the frontal, lacrimal, ethmoid, zygomatic, maxillary, and palatine, and sphenoid bones. Can you think of any part of the human body where seven bones converge to fulfill a singular purpose? In recognition of this phenomenal feature of the human anatomy (and one of the most recognizable parts of the human skull), this week's embodi3D® Top Uploads articles, we are featuring several standout uploads — all of which can be used to create an orbital and skull 3D model. As detailed in the scholarly article "Clinical application of three-dimensional printing technology in craniofacial plastic surgery" 3D printing techniques are being used in craniofacial surgeries and especially in reconstruction procedures the require complex modeling. Using the latest 3D printing technology and the STL files converted using democratiz3D®, the contralateral orbit can serve as a point of reference for those in the medical field since the ipsilateral structures taken with a CT scan can be easily converted into an STL file and then fed to a 3D printer. These technologies improve patient consultations, increase the quality of diagnostic information while also helping to improve the planning stage of the surgical process. During surgery, a 3D-printed model of the orbital can be used to orient surgical staff and serve as a guide for surgical resectioning procedures. While these files are available for free on the website, you must register with embodi3D® before you can begin uploading and converting your own CT scans into STL files as well as downloading and 3D printing anatomical models from other users. Every day the collection of anatomical models grows on the embodi3D® website. This is but one of the many ways embodi3D® is seeking to revolutionize medical practices. #1. An Awesome Model of the Orbit's Acute Anatomy The orbits are conical structures dividing the upper facial skeleton from the middle face and surround the organs of vision. Seven bones conjoin to form the orbital structure as we can see in the example below. #2. A 3D Model of the Orbit's Surface in STL Format This excellent 3D model of embodi3D® shows the superficial bony margin of the orbit, which is rectangular with rounded corners. The margin is discontinuous at the lacrimal fossa. The supraorbital notch (seen in the image below) is within the supraorbital rim and is closed to form the supraorbital foramen in 25% of individuals. The supratrochlear notch is medial to the supraorbital notch. #3. A CT Scan of an Orbital Floor Fracture Hisham published this excellent ct scan on embodi3D®. Direct fractures of the orbital floor can extend from fractures of the inferior orbital rim. Indications for repair of the orbital floor in these cases are the same as those for indirect (blowout) fractures. Indirect fractures of the orbital floor are not associated with fracture of the inferior orbital rim. #4. A 3D Model of an Orbital Fracture CT scans with coronal or sagittal views and 3D models help guide treatment. They allow evaluation of fracture size and extraocular muscle relationships, providing information that can be used to help predict enophthalmos and muscle entrapment. #5. 3D Model Showing an Orbital Fracture Dropbear upload this excellent example of a right orbit fracture. #6. An Orbit 3D Model (Printable) Showing Fibrous Dysplasia (FD) for Surgical Demonstration The FD is a benign slowly progressive disorder of bone, where normal cancellous bone is replaced by fibrous tissue and immature woven bone. This entity constitutes about 2.5 % of all bone tumors. References Choi, J. W., & Kim, N. (2015). Clinical application of three-dimensional printing technology in craniofacial plastic surgery. Archives of plastic surgery, 42(3), 267. Bibby, K., & McFadzean, R. (1994). Fibrous dysplasia of the orbit. British journal of ophthalmology, 78(4), 266-270.
  3. Segmentation of a foot MRI scan

    Hello Mike! I have done several tests using Fast GrowCut and I have obtained an .stl file but effectively with contours necessarily far from the precision of a bone, so it is necessary to soften. You comment that you use a MatLab code to perform the smoothing of the bones, could you send us the MatLab code that you use to soften the volume of the 3D model obtained from MRI. Thank you very much in advance.
  4. How to Easily Tell the Difference Between MRI and CT Scan

    Great blog! Its the easiest way in which someone must have explained the difference between CT scan and MRI scan. Thanks for sharing such a wonderful blog, most of the people would like it. I would also like to know the difference between Ultrasound, MRI, and CT scan.
  5. 3D-Printed Models of the Spine In this week's post, we want to share with you some of the best 3D-printed models of the spine uploaded by embodi3D® members. We will explore features of this unique anatomy and some of the main uses of 3D printing as it relates to the spine . To convert your own scans and download and 3D-print STL files from other users, all you have to do is register with embodi3D®. It's quick, easy, and costs absolutely nothing to join. Anatomical models have applications in clinical training and surgical planning as well as in medical imaging research. The Wall Street Journal recently ran an article to discuss the many ways 3D printing is changing the face of healthcare. The article also highlighted a case where a 3D model of a pelvis was used to plan a surgical operation on a young female patient. A full-scale, anatomical model of a human lumbar vertebra created with embodi3D®. In terms of clinical applications, the physical interaction with models facilitates learning anatomy and how different structures interact spatially in the body. Simulation-based training with anatomical models reduces the risks of surgical interventions, which are directly linked to patient experience and healthcare costs. Surgical planning 3D printing (3DP) is most frequently utilised in spinal surgery in the pre-operative planning stage. A full-scale, stereoscopic understanding of the pathology allows for more detailed planning and simulation of the procedure. Assessing complex pathologies on a model overcomes many of the issues associated with traditional 3D imaging, such as the lack of realistic anatomical representation and the associated complexity of computer-related skills and techniques. Summary of 3DP in spinal surgery planning 1999 D’Urso et al. (4) Osteogenesis imperfecta, cervicothoracic deformity, lumbar spinal fusion, cervical osteoblastoma 1999 D’Urso et al. (5) Craniofacial, maxillofacial and skull base cervical spine pathologies. 2005 D’Urso et al. (6) Complex spinal disorders. 2007 Guarino et al. (7) Multiplane spinal and pelvic deformities. 2007 Izatt et al. (8) Deformities, spinal tumours. 2007 Paiva et al. (9) Cervical Ewing Sarcoma. 2008 Mizutani et al. (10)Rheumatoid cervical spine. 2009 Madrazo et al. (11)Degenerative cervical disease. 2010 Mao et al. (12) Kyphoscoliosis, congenital malformations, neuromuscular disease. 2010 Yang et al. (13) Kyphoscoliosis. 2011 Wu et al.(14) Severe congenital scoliosis. 2013 Toyoda et al. (15) Atlantoaxial subluxation. 2014 Yang et al. (16) Atlantoaxial instability. 2015 Li et al.(17) Revision lumbar discectomy. 2015 Kim et al. (18)Thoracic tumours. 2015 Sugimoto et al. (19) Congenital kyphosis. 2015 Yang et al. (20) Adolescent idiopathic scoliosis. 2016 Goel et al. (21) Craniovertebral junction anomalies. 2016 Wang et al. (22) Congenital scoliosis, atlas neoplasm, atlantoaxial dislocation. 2016 Xiao et al. (23) Cervical bone tumours. 2017 Guo et al. (24) Cervical spine diseases. Imaging Anatomy There are 33 spinal vertebrae, which comprise two components: A cylindrical ventral bone mass, which is the vertebral body,and the dorsal arch. 7 cervical, 12 thoracic, 5 lumbar bodies • 5 fused elements form the sacrum • 4-5 irregular ossicles form the coccyx Arch • 2 pedicles, 2 laminae, 7 processes (1 spinous, 4 articular, 2 transverse) • Pedicles attach to the dorsolateral aspect of the body • Pedicles unite with a pair of arched flat laminae • Lamina capped by dorsal projection called the spinous process • Transverse processes arise from the sides of the arches The two articular processes (zygapophyses) are diarthrodial joints. • (1) Superior process bearing a facet with the surface directed dorsally • (2) Inferior process bearing a facet with the surface directed ventrally Pars interarticularis is the part of the arch that lies between the superior and inferior articular facets of all subatlantal movable elements. The pars are positioned to receive biomechanical stresses of translational forces displacing superior facets ventrally, whereas inferior facets remain attached to dorsal arch (spondylolysis). C2 exhibits a unique anterior relation between the superior facet and the posteriorly placed inferior facet. This relationship leads to an elongated C2 pars interarticularis, which is the site of the hangman's fracture. 1. An Exceptional Human Lumbar Vertebra Converted from a CT Scan with embodi3D® An anatomically accurate full-size human lumbar vertebra created from a real CT scan. The lumbar vertebral bodies are large, wide and thick, and lack a transverse foramen or costal articular facets. The pedicles are strong and directed posteriorly. The superior articular processes are directed dorsomedially and almost face each other. The inferior articular processes are directed anteriorly and laterally. 2. Create Your Own Lumbar Spine Model with a 3D-Printable STL File A 3D printable STL file and medical model of the lumbar spine was generated from real CT scan data and is thus anatomically accurate as it comes from a real person. It shows the detailed anatomy of the lumbar (lower back) spine, including the vertebral bodies, facets, neural foramina and spinous proceses. 3. A 3D Printer-Ready Spinal Column in Amazing Detail Thoracic bodies are heart-shaped and increase in size from superior to inferior. Facets are present for rib articulation and the laminae are broad and thick. Spinous processes are long, directed obliquely caudally. Superior facets are thin and directed posteriorly. The T1 vertebral body shows a complete facet for the capitulum of the first rib, and an inferior demifacet for capitulum of second rib. The T12 body has transitional anatomy, and resembles the upper lumbar bodies with the inferior facet directed more laterally 4. Create a 3D-Printed Model of Lumbar Vertebrae The lumbar spine is formed by 5 lumbar vertebrae labelled L1-L5 and the intervening discs. Its main function is to provide stability and permits movement. The lumbar vertebral body is formed of 3 parts : Body, arch and spinal processes. The body of the lumbar vertebrae is large, its transverse diameter is larger than is AP diameter, and is more thickened anteriorly. The arch of the lumbar vertebra on the other hand is formed of pedicle, a strong structure that is projected from the back of the upper part of the vertebrae, and lamina which forms the posterior portion of the arch. Another well reported benefit of 3DP models is improved patient education. A physical model is much easier for a patient to understand than complex MRI and CT scans. 5. An NRRD File Showing the Whole Spine — See the Future of Medical 3D Printing A Whole Spine (Dorsal-Lumbar-Sacral) and Aorta NRRD file from CT Scan for Medical 3D Printing As 3DP technology continues to become cheaper, faster and more accurate, its use in the setting of spinal surgery is likely to become routine, and in a greater number of procedures. 6. Download a 3D-Printable Thoracic Spine with Prevalent Scoliosis A 3D printable STL file contains a model of the thoracic spine derived from a CT. The spine has significant scoliosis. In a recent embodi3D® article, we touched on the topic of how medical 3D printing is being used to plan spinal surgeries, such as in correcting the spinal curvature in scoliosis patients. Scoliosis is considered to be present when there is a coronal plane curvature of the spine measuring at least 10°. However, treatment is not generally instituted unless the curvature is > 20-25°. The curvature may be balanced (returning to midline) or unbalanced. The vertebrae at the ends of the curve are designated the terminal (or end) vertebrae, while the apical vertebra is at the curve apex. Curvatures are described by the side to which they deviate. A dextroscoliosis is convex to the right, with its apex to the right of midline. A levoscoliosis is convex to the left, with its apex to the left of midline. Curvatures can be categorized as flexible (normalizing with lateral bending toward the side of the curve) or structural (failing to correct). Most scoliotic curvatures are associated with abnormal curvature in the sagittal plane. These are described as kyphosis (apex dorsal) or lordosis (apex ventral). Morphology of the Curvature Scoliosis due to fracture, congenital anomaly, or infection typically has an angular configuration. Other causes of scoliosis tend to have a smooth curvature. Scoliosis most commonly involves the thoracic spine, followed by the thoracolumbar spine. In the past, curves were categorized as primary and secondary (compensatory), but it is often difficult to make the distinction and so these designations are no longer commonly used. Measurement of Scoliosis The Cobb method is most commonly used to measure scoliosis. The vertebrae at each end of the curve (the terminal vertebrae) are chosen. These are the endplates with the greatest deviation from the horizontal. The curvature is the angle between a line drawn along the superior endplate of superior terminal vertebra and a line along the inferior endplate of the inferior terminal vertebra. In severe curvatures, the endplates are often difficult to see. In that case, the inferior cortex of the pedicle can be used as the landmark for making the measurement. If measurements are made on hard copy radiographs, it is usually necessary to draw lines perpendicular to the endplates and measure the angle between the perpendicular lines. Scoliosis is almost always associated with abnormal curvature in the sagittal plane. The most common finding is loss of normal thoracic kyphosis. The Cobb method can be used to determine sagittal plane deformity. Rotational deformity is often present but can only be grossly assessed on radiographs. It can be measured on CT scan by superimposing the apical and terminal vertebrae. Normally, the T1 vertebra is centered over the L5 vertebra in both the coronal and sagittal planes. Coronal or sagittal plane imbalance can be measured as the horizontal distance between the center of the L5 vertebral body and a plumb line drawn through the center of the T1 vertebral body. 7. Dr. Mike's Excellent Tutorial on Converting CT Scans to 3D Printer-Ready STL Models An excellent tutorial of A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes which allows you to follow along with the tutorial. Included is an anonymized chest abdomen pelvis CT in both DICOM and NRRD formats. 8. An MRI of a Lumbar Spine with Disc Bulge at L4-L5 and L5-S1 The term bulge is used to describe a generalized extension greater than 50% of the circumference of the disc tissues, extending a short distance (< 3 mm) beyond the edges of the adjacent apophyses. A bulge is not a herniation, although 1 portion of the disc may be bulging and another portion of the disc may herniate. A bulge is often a normal variant, particularly in children in whom all normal discs appear to extend slightly beyond the vertebral body margin. Bulge may also be associated with disc degeneration or may occur as a response to axial loading or angular motion with ligamentous laxity. Occasionally, a bulge in 1 plane is really a central subligamentous disc herniation in another plane. Asymmetric bulging of disc tissue greater than 25% of the disc circumference may be seen as an adaptation to adjacent deformity, and is not considered a form of herniation. Herniations are a localized displacement of disc material beyond the limits of the intervertebral disc space in any direction. 9. Using 3D Modeling to Understand the Severity of a Scoliosis Case A 3D model of a severe scoliosis. CT scan should always be performed with reformatted images. Angled reformatted images and 3D reformations are often useful in assessment of severe curvatures. Some physicians find it useful to obtain both SPECT and CT images of degenerative scoliosis. An area of arthritis on CT scan, which shows increased uptake on SPECT, is probably a pain generator. MR can be difficult to interpret when scoliosis is severe. Angled axial images should be obtained based on both sagittal and coronal scout images and angled along the plane of the vertebral endplate on both scouts. Sagittal images should be angled along each segment of the curvature. The coronal plane is often the most useful for evaluating bony anomalies, spondylolysis, or degeneration of the discs and facet joints. References 1. Bücking, T. M., Hill, E. R., Robertson, J. L., Maneas, E., Plumb, A. A., & Nikitichev, D. I. (2017). From medical imaging data to 3D printed anatomical models. PloS one, 12(5), e0178540. 2. Wilcox, B., Mobbs, R. J., Wu, A. M., & Phan, K. (2017). Systematic review of 3D printing in spinal surgery: the current state of play. Journal of Spine Surgery, 3(3), 433. 3. Ross, J. S., Moore, K. R., Bryson Borg, M. D., Julia Crim, M. D., & Shah, L. M. (2010). Diagnostic imaging: spine: published by Amirsys®. Lippincott Williams & Wilkins, Baltimore. 4. D'Urso PS, Askin G, Earwaker JS, et al. Spinal biomodeling.Spine (Phila Pa 1976) 1999;24:1247-51. 10.1097/00007632-199906150-00013. 5. D'Urso PS, Barker TM, Earwaker WJ, et al. Stereolithographic biomodelling in cranio-maxillofacial surgery: a prospective trial. J Craniomaxillofac Surg 1999;27:30-7. 10.1016/S1010-5182(99)80007-9 6. D'Urso PS, Williamson OD, Thompson RG. Biomodeling as an aid to spinal instrumentation. Spine (Phila Pa 1976) 2005;30:2841-5. 10.1097/01.brs.0000190886.56895.3d 7. Guarino J, Tennyson S, McCain G, et al. Rapid prototyping technology for surgeries of the pediatric spine and pelvis: benefits analysis. J Pediatr Orthop 2007;27:955-60. 10.1097/bpo.0b013e3181594ced 8. Izatt MT, Thorpe PL, Thompson RG, et al. The use of physical biomodelling in complex spinal surgery. Eur Spine J 2007;16:1507-18. 10.1007/s00586-006-0289-3 9. Paiva WS, Amorim R, Bezerra DA, et al. Aplication of the stereolithography technique in complex spine surgery. Arq Neuropsiquiatr 2007;65:443-5. 10.1590/S0004-282X2007000300015 10. Mizutani J, Matsubara T, Fukuoka M, et al. Application of full-scale three-dimensional models in patients with rheumatoid cervical spine. Eur Spine J 2008;17:644-9. 10.1007/s00586-008-0611-3 11. Mao K, Wang Y, Xiao S, et al. Clinical application of computer-designed polystyrene models in complex severe spinal deformities: a pilot study. Eur Spine J 2010;19:797-802. 10.1007/s00586-010-1359-0 12. Yang JC, Ma XY, Lin J, et al. Personalised modified osteotomy using computer-aided design-rapid prototyping to correct thoracic deformities. Int Orthop 2011;35:1827-32. 10.1007/s00264-010-1155-9 13. Wu ZX, Huang LY, Sang HX, et al. Accuracy and safety assessment of pedicle screw placement using the rapid prototyping technique in severe congenital scoliosis. J Spinal Disord Tech2011;24:444-50. 10.1097/BSD.0b013e318201be2a 14. Toyoda K, Urasaki E, Yamakawa Y. Novel approach for the efficient use of a full-scale, 3-dimensional model for cervical posterior fixation: a technical case report. Spine (Phila Pa 1976)2013;38:E1357-60. 10.1097/BRS.0b013e3182a1f1bd 15. Yang JC, Ma XY, Xia H, et al. Clinical application of computer-aided design-rapid prototyping in C1-C2 operation techniques for complex atlantoaxial instability. J Spinal Disord Tech 2014;27:E143-50. 16. Li C, Yang M, Xie Y, et al. Application of the polystyrene model made by 3-D printing rapid prototyping technology for operation planning in revision lumbar discectomy. J Orthop Sci 2015;20:475-80. 10.1007/s00776-015-0706-8 17. Kim MP, Ta AH, Ellsworth WA, 4th, et al. Three dimensional model for surgical planning in resection of thoracic tumors. Int J Surg Case Rep 2015;16:127-9. 10.1016/j.ijscr.2015.09.037 18. Sugimoto Y, Tanaka M, Nakahara R, et al. Surgical treatment for congenital kyphosis correction using both spinal navigation and a 3-dimensional model. Acta Med Okayama 2012;66:499-502. 19. Yang M, Li C, Li Y, et al. Application of 3D rapid prototyping technology in posterior corrective surgery for Lenke 1 adolescent idiopathic scoliosis patients. Medicine (Baltimore) 2015;94:e582. 10.1097/MD.0000000000000582 20. Goel A, Jankharia B, Shah A, et al. Three-dimensional models: an emerging investigational revolution for craniovertebral junction surgery. J Neurosurg Spine 2016;25:740-4. 10.3171/2016.4.SPINE151268 21. Wang YT, Yang XJ, Yan B, et al. Clinical application of three-dimensional printing in the personalized treatment of complex spinal disorders. Chin J Traumatol 2016;19:31-4. 10.1016/j.cjtee.2015.09.009 22. Xiao JR, Huang WD, Yang XH, et al. En Bloc Resection of Primary Malignant Bone Tumor in the Cervical Spine Based on 3-Dimensional Printing Technology. Orthop Surg 2016;8:171-8. 10.1111/os.12234 23. Guo F, Dai J, Zhang J, et al. Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine. PLoS One 2017;12:e0171509. 10.1371/journal.pone.0171509
  6. Dear Dr Mike, We used this workflow in our facility to make a tibial fracture model. By doing so, printing time was reduced from 26hr to 13hr (using uPrint SE plus) without loosing details. Thank you for the great tutorial and educational materials, Itamar
  7. This week we would like to share the most downloaded 3D models and resources from our site. These may be good resources for educational purposes as they demonstrate the detailed anatomy of the human body. We have a list of the top human heart STL files and another list of free human anatomy STL files. The 1st place is for Dr. Mike’s tutorial on how to create 3D printable bone models. 3D printing is an evolving technology that enables the creation of unique organic and inorganic structures with high precision. In medicine, this technology has demonstrated potential uses for both patient treatment and education as well as in clinical practice. Learning how to create 3D models and taking this technology as a great advantage for medical education and practice is important for all of us as physicians and this tutorial makes it easy to learn. The list also includes other great 3D models, like skull and heart. Let’s then take a look into this ten awesome models. Don’t forget to register in order to download the models, you can do it by clicking here. 1. 2.952 Downloads An improved tutorial that shows you how to create 3D printable bone models even more easily and for free on any operating system. Try it! https://www.embodi3d.com/files/file/115-file-pack-for-3d-printing-with-osirix-tutorial/ 2. 913 Downloads 3D printable model of a human heart was generated from a contrast enhanced CT scan. https://www.embodi3d.com/files/file/64-3d-printable-human-heart-model-with-stackable-slices/ 3. 893 Downloads 3D printable brain is from an MRI scan of a 24 year old human female. https://www.embodi3d.com/files/file/30-human-brain-from-mri-scan/ 4. 714 Downloads This full-size skull with web-like texture was created from a real CT scan. https://www.embodi3d.com/files/file/26-3d-printable-lace-skull-full-size/ 5. 648 Downloads 3D printable model of stroke. https://www.embodi3d.com/files/file/6378-3d-printing-brain-model-with-stroke-stl-files-available-for-download/ 6. 609 Downloads Skull with web-like texture was created from a real CT scan. https://www.embodi3d.com/files/file/25-3d-printable-lace-skull-half-size/ 7. 422 Downloads Anatomically accurate heart and pulmonary artery tree was extracted from a CT angiogram. https://www.embodi3d.com/files/file/59-heart-and-pulmonary-artery-tree-from-ct-angiogram/ 8. 396 Downloads Tutorial: "3D Printing of Bones from CT Scans: A Tutorial on Quickly Correcting Extensive Mesh Errors using Blender and MeshMixer” https://www.embodi3d.com/files/file/89-tutorial-file-pack/ 9. 392 Downloads Tutorial A Ridiculously Easily Way to Convert CT Scans to 3D Printable Bone STL Models for Free in Minutes https://www.embodi3d.com/files/file/6441-imag3d-tutorial-support-files-dicom-and-nrrd/ 10. 373 Downloads Bony anatomy and skin surface of the L and R feet. https://www.embodi3d.com/files/file/52-feet-from-ct-scan/ References 1. Colaco, M., Igel, D. A., & Atala, A. (2018). The potential of 3D printing in urological research and patient care. Nature Reviews Urology.
  8. Segmentation of a foot MRI scan

    I haven't checked it out recently but I will, thank you! I'm a big fan of 3DSlicer. I'll let you know if I have any questions.
  9. Segmentation of a foot MRI scan

    Have you tried 3D Slicer recently? We've completely reworked segmentation by adding a new Segment Editor, which should be comparable and in a couple of things much better than commercial software (not just in price, flexibility and extensibility but in capabilities as well). Segment editor supports overlapping segments, advanced masking, real-time slice/3D view synchronization, hugely improved Fast GrowCut ("Grow from seeds"), contour interpolation, hollowing, smoothing, cutting, Boolean operations, input volume switching, editing on oblique slices, etc. You can find a couple of tutorials and demos on our lab's YouTube channel and you can find some step-by-step tutorials here. If you install SlicerRT extension, then you can load RT structure sets directly into Slicer and edit them using Segment Editor (or compare them, register, transform them, export them to DICOM, compute DVH, etc.). See for example this module for DICOM import, automatic registration of prostate MRI to ultrasound, and DICOM export: If you have any specific request or recommendation then let us know. There may be many things that are easy to implement and make your work much easier.
  10. Hi Devarsh, I am working on a Color MRI software for viewing and interpretting MRI images. It is a free and opensource plugin for Osirix image viewer, which works on MacOs. You can download the plugin here. Plugin main page and documentation is here. It is in alpha phase and has known issues. Please feel free to report additonal bugs while being the first using it. The plugin generates 24bit color images in which fat is yellow, water is cyan and muscles are dark red. One of the secondary benefits I expect from plugin is better segmentation from MRI data. Fat, muscle and water each will have distinct colors and should be easy for segmentation. The other advancement I expect from Osirix Color MRI plugin is the creation of Color medical 3D prints from MRI data. Nevit Note: Dr. Mike's tutorial has good introductory info about Osirix. Sample Color MRI image:
  11. Intellectual property protection

    I shared one of my models with an acquaintance of mine, because he wanted to test his new Prusa 3D printer with it. Later he posted it on a website for selling. I approached the problem personally, he removed the model from the site and apologized to me, this is why I won't share details about the issue (he had to print some of my models for free, of course). Now all my models are watermarked and if I have such a case, I can contact the administrator instead, my name and my institution are inserted in the mesh itself.
  12. hello...i did all the steps to crop de dicom surce file....but there isn t a crop button in the latest 3d slicer version....how can i saved just the cropped part ? i tried to and upload it to democratiz3d but there ws some kinf of error...
  13. Intellectual property protection

    Thanks for the reference. Can you elaborate on the IP theft you mentioned? What happened?
  14. Intellectual property protection

    The protection of the intellectual property of the 3D models can be a serious issue for every 3D modeler. It sucks when your model is posted for selling at a webside without your consent with a juicy price and you're gaining NOTHING from it. Some 3D artists are adding watermarks to their models, which can be easily removed by an amateur with a free surface modelling program (Meshmixer, Meshlab etc.). But there is an easy solution for this injustice - an invisible watermark. On Watermark3D you can add such watermark, incorporated into the mesh of your 3D model itself, which is hard for removing and can be checked on the same website during an intellectual property dispute. For the removing of the watermark you have to remesh the whole model, which will decrease the overall quality of the model substantially. I hope that I'll spare you the pain, which I experienced recently. Enjoy
  15. Hello the Biomedical 3D Printing community, it's Devarsh Vyas here writing after a really long time! This time i'd like to share my personal experience and challenges faced with respect to medical 3D Printing from the MRI data. This can be a knowledge sharing and a debatable topic and I am looking forward to hear and know what other experts here think of this as well with utmost respect. In the Just recently concluded RSNA conference at Chicago had a wave of technology advancements like AI and 3D Printing in radiology. Apart from that the shift of radiologists using more and more MR studies for investigations and the advancements with the MRI technology have forced radiologists and radiology centers (Private or Hospitals) to rely heavily on MRI studies. We are seeing medical 3D Printing becoming mainstream and gaining traction and excitement in the entire medical fraternity, for designers who use the dicom to 3D softwares, whether opensource or FDA approved software know that designing from CT is fairly automated because of the segmentation based on the CT hounsifield units however seldom we see the community discuss designing from MRI, Automation of segmentation from MRI data, Protocols for MRI scan for 3D Printing, Segmentation of soft tissues or organs from MRI data or working on an MRI scan for accurate 3D modeling. Currently designing from MRI is feasible, but implementation is challenging and time consuming. We should also note reading a MRI scan is a lot different than reading a CT scan, MRI requires high level of anatomical knowledge and expertise to be able to read, differentiate and understand the ROI to be 3D Printed. MRI shows a lot more detailed data which maybe unwanted in the model that we design. Although few MRI studies like the contrast MRI of the brain, Heart and MRI angiograms can be automatically segmented but scans like MRI of the spine or MRI of the liver, Kidney or MRI of knee for example would involve a lot of efforts, expertise and manual work to be done in order to reconstruct and 3D Print it just like how the surgeon would want it. Another challenge MRI 3D printing faces is the scan protocols, In CT the demand of high quality thin slices are met quite easily but in MRI if we go for protocols for T1 & T2 weighted isotropic data with equal matrix size and less than 1mm cuts, it would increase the scan time drastically which the patient has to bear in the gantry and the efficiency of the radiology department or center is affected. There is a lot of excitement to create 3D printed anatomical models from the ultrasound data as well and a lot of research is already being carried out in that direction, What i strongly believe is the community also need advancements in terms of MRI segmentation for 3D printing. MRI, in particular, holds great potential for 3D printing, given its excellent tissue characterization and lack of ionizing radiation but model accuracy, manual efforts in segmentation, scan protocols and expertise in reading and understanding the data for engineers have come up as a challenge the biomedical 3D printing community needs to address. These are all my personal views and experiences I've had with 3D Printing from MRI data. I'm open to and welcome any tips, discussions and knowledge sharing from all the other members, experts or enthusiasts who read this. Thank you very much!
  16. Hi, Mike. What type of resins do you use for your medical prints?
  17. Hello everybody it's Dr. Mike here again with another medical 3D printing tutorial. In this tutorial we are going to be going over freeware and open-source software options for medical 3D printing. This tutorial is based on a workshop I am giving at the 2017 Radiological Society of North America (RSNA) Annual Meeting in Chicago Illinois, November 2017. In this tutorial we will be going over desktop software that can be used to create 3D printable anatomic models from medical scans, as well as a free online automated conversion service. At the end of this tutorial you should be able to make high-quality 3D printable models from a medical imaging scan using free software or services. Do I need to use FDA-approved software for Medical 3D Printing? Before I dive into the tutorial I'd like to take a minute to talk to learners from the United States about the US Food and Drug Administration (FDA) and how this federal agency impacts medical 3D printing. Many healthcare professionals are confused and concerned about the ability to use non-FDA-approved software for medical 3D printing. Software vendors sell software that has been FDA-approved, but the software is usually quite expensive, to the tune of many thousands of dollars per year in license fees. There has been a lot of confusion about whether non-FDA-approved free software can be used for medical applications. In August 2017 a meeting was held at the main FDA campus between FDA staff and representatives from RSNA. During this meeting the FDA clarified its stance on the issue (Figure 1). Basically the FDA indicated that if a doctor needs a 3D printed model for patient care, the doctor does NOT need to use FDA-approved software, as this is a medical decision and the FDA does not regulate the practice of medicine. FDA-approved software is not required even if the doctor is using the model for diagnostic use (Figure 2). If a company or other organization is marketing or designing software for diagnostic use, then that company or organization is required to seek FDA approval for that product. Basically if you are a physician or working on behalf of the physician and require a model, FDA-approved software is not required as long as you are not running a commercial service or company. Despite this leeway granted by the FDA's interpretation, I encourage anyone considering using freeware to create models for diagnostic use to use common sense and double check your findings before making any critical decision that could impact patient care. I also encourage you to look at the slides from the FDA presentation directly at the link below. Of course, none of this applies if you are not creating models for medical use. https://www.fda.gov/downloads/MedicalDevices/NewsEvents/WorkshopsConferences/UCM575723.pdf Figure 1: Title slide from the FDA presentation Figure 2: The relevant slide from the FDA presentation. Doctors creating 3D printable models for clinical and diagnostic use do not need to use FDA-approved software as this is considered practice of medicine, which the FDA does not regulate. Medical 3D Printing Overview In this tutorial we're going to go over two different ways to use free and open-source software to convert a medical imaging scan to a 3D printable model. This can be done using free desktop software or a free online service. The desktop software requires more steps and more of a learning curve, but also allows more control for customized models. The online service is fast, easy, and automated. However, if you want to design customized elements into your model, you'll not be able to. The overall workflow of the session is shown in Figure 3. Figure 3: Workflow overview Part 1: Free online service – embodi3D.com Step 1: Download the scan Please download the scan for this tutorial from the embodi3D.com website at the link below. You have to have a free embodi3D.com account in order to download. If you don't have an account go ahead and register by clicking on the "Sign Up" button on the upper right-hand portion of the page. Registration is easy and only takes about one minute. You will have to confirm your email address before your account is active, so make sure you have access to your email. Step 2: Inspect the scan If you don't already have it, download and install the desktop software program 3D Slicer from slicer.org (http://www.slicer.org/). Slicer is a free medical image viewing and research software application. We are going to use Slicer to view our scan. Once Slicer is installed, open the application. Drag-and-drop the file "CTA Head.nrrd" onto the Slicer window. Slicer will ask if you want to add the file, click OK. The scan should now show in Figure 4. If your window doesn't look this then select the Four Up layout from the Layouts drop-down menu. Figure 4: The 4 panel view and Slicer You can navigate and manipulate the images with Slicer using the various mouse buttons. Your left mouse button to adjust the window/level settings as shown in Figure 5. Figure 5: Use the left mouse button to adjust window/level. The right mouse button allows you to zoom into a specific panel, as shown in Figure 6. Figure 6: The right mouse button controls zoom. The scroll wheel allows you to move through the various slices of the scan, as shown in Figure 7. Figure 7: The mouse wheel controls scrolling Step 3: Upload the scan to embodi3D.com Now that we have an idea about what's in the scan, you can upload it to embodi3D.com for automatic processing into a 3D printable model. Go to https://www.embodi3d.com/. If you don't yet have a free embodi3D.com user account, you will need one now. Go ahead and register. The process only takes a minute. Under the democratiz3D menu, click Launch App, as shown in Figure 8. Figure 8: Launching the democratiz3D medical scan to 3D printable model automated conversion service. Drag and drop the file "CTA Head.nrrd" onto the upload panel, as shown in Figure 9. The NRRD file format is an anonymized file format so this transfer is HIPAA compliant. If you want to know more about how to create an NRRD file from a DICOM data set, please see my tutorial on the topic here. Figure 9: Drag-and-drop the scan file "CTA Head.nrrd" onto the highlighted upload panel A submission form will open up. The first part of the form will ask you questions about the source file you're uploading. The second part will ask about the new model being generated. Start with the first part of the form, as shown in Figure 10, and fill in information about your uploaded scan file, including a filename, short description, any tags you wish to use to help people identify your file, whether you wish to share the file with the community or keep it private, and whether you want to make the file free for download or for sale. Obviously if you keep the file private this last setting doesn't matter as nobody will be able to see the file except you. Figure 10: The first part of the form relates to information about your uploaded scan file. Make sure you fill in at least the required elements. In the second part of the form fill in information about your model file that will be generated, as shown in Figure 11. First of all, make sure democratized processing is turned on. The slider should be green in color, as shown in Figure 11. This is very important because if processing is turned off, you will not generate an output model file! Specify what operation you would like to perform on the scan, and whether you would like to generate a bone, muscle, or skin model. Also, specify the desired quality of the output model (low, medium, high, etc.) and whether you want the output model to be shared with the community (recommended) or private. If your file is going to be shared, choose a Creative Commons license that people can use it under. When you're satisfied with your parameters, click the Submit button. Figure 11: The second part of the form relates to information about your 3D printable model to be generated. Choose an operation, quality level, as well as privacy settings. Step 4: Download your finished 3D printable model. After anywhere between 5 to 20 minutes you should receive an email saying that your model processing is complete. The exact time depends on a variety of factors including the complexity of your model, the quality that you've chosen, as well as server load. Once you receive the email follow the link to the model download page. Alternatively you can find the model by clicking on your username at the upper right-hand corner of any embodi3D.com webpage and selecting My Files. Once you find your model page you can inspect the thumbnails to make sure the model meets your criteria, as shown in Figure 12. When you are ready click the download button, agree to the terms, and your model STL file will download to your computer. Figure 12: Download your file after processing is complete. That's it! Your 3D printable model is ready to send to a printer. The process takes about 2 to 3 minutes to enter the data, plus 5 to 15 minutes to wait for the processing to be done. The embodi3D.com service is batchable, so it is possible for you to upload multiple files simultaneously. The service will crank out models as fast as you can upload them. Part 2: Free desktop software – 3D Slicer and Meshmixer You can use the free software program 3D slicer and Meshmixer to generate 3D printable models. The benefit of using desktop software is that you have more control over the appearance of the model and which structures you want included and excluded. The downside of using desktop software is that software is complicated and somewhat time-consuming to learn. If you haven't already download 3D Slicer and Meshmixer from the links below. Be sure to choose the appropriate operating system for your computer. http://www.slicer.org/ http://meshmixer.com/ Step 1: Download the tutorial scan file and load into Slicer as described above in Part 1 Steps 1 and 2. Step 2: Create a surface model from the scan data. From within Slicer, open the Grayscale Model Maker module. In the Modules menu at the top now bar, select All Modules and choose the Grayscale Model Maker item, as shown in Figure 13. Figure 13: Selecting the Grayscale Model Maker module. You will now be taken to the Grayscale Model Maker module, which will convert the volumetric data in the CT scan to a surface model that can be used to create a STL file for 3D printing. In the parameters panel on the left side of the screen, make sure that the parameter set value is set to "Grayscale Model Maker", and the Input Volume is set to "CTA Head." Under Output Geometry, choose Create a New Model, since we wish to create a new output model. These parameters are shown in Figure 14. Figure 14: Input parameters for the Grayscale Model Maker module Set the Threshold value to 150 Hounsfield units. Also, set the Decimate value to 0.8 and make sure the Split Normals checkbox is unchecked. These are shown in Figure 15. When you're happy with your parameters, check Apply, and the grayscale model maker will work for a minute or so to create your surface model. Figure 15: Additional input parameters for the Grayscale Model Maker module Step 3: Save the surface model to an STL file. Now that you have generated a surface model, you are ready to export it to an STL file. Click on the Save button on the upper left-hand corner of the 3D Slicer window. A Save dialog box will pop up, as shown in Figure 16. Find the row that contains the item "Output Geometry.vtk." Make sure that the checkbox next to this item is checked. All other rows should be unchecked. In the File Format column, make sure that the file shows as STL. Finally, make sure that the directory specified in the third column is the one you wish to save the file to. When everything is correct go ahead and click Save. Your surface model will now be exported and STL file saved in the directory specified. Figure 16: The Save dialog box Step 4: Repair the model in Meshmixer The model is in STL format, but it has multiple errors in it which need to be corrected prior to 3D printing. We will do this in the freeware software program Meshmixer. Open Meshmixer, and drag-and-drop the just-created STL file "Output Geometry.stl" onto the Meshmixer window. The model will now open in Meshmixer. You will notice that the model is quite large, having about 300,000 polygons, as shown in Figure 17. Figure 17: Open the model in Meshmixer Navigating in Meshmixer is quite intuitive. The left mouse button uses tools and selects structures. The right mouse button is used to rotate the model. The scroll wheel is used to zoom in and out, as shown in Figure 18. Figure 18: Navigating in Meshmixer Run an initial repair on the model using the Inspector tool We will be able to get rid of most (but not all) errors using the automated Inspector tool. Click on the Analysis button on the left navigation pane and choose the Inspector tool. Inspector will run and highlight all of the problems with the model, as shown in Figure 19. As you can see there are many hundreds of errors. Click on the Auto Repair All button to automatically attempt to fix these. At least one error will remain after the end of the process, but don't worry we will fix that later. Click on the Done button. Figure 19: The Inspector tool shows errors in the mesh Remesh the model The Remesh operation recalculates all the polygons in the model, adjusting their size, and giving the model in more natural and less faceted look. Remesh and can also help to fix lingering mesh errors. First, select all the polygons in the model by hitting control-A. The entire model should turn orange, as shown in Figure 20. Figure 20: Selecting all the polygons in the model. Next, run the Remesh operation. Hit the R key, or choose Select-> Edit-> Remesh. The Remesh operation will now run, and will take approximately 1.5 to 2 minutes, depending on the power of your computer. This is shown in Figure 21. Figure 21: The Remesh operation. At the end of the Remesh operation, your model should have a much smoother and more natural appearance. You can adjust some of the Remesh parameters in the visualized pane, and the operation will recalculate. When you're happy with the result, click on the Accept button. This is shown in Figure 22. Figure 22: The model after the Remesh operation. Repeat the Inspector tool operation Now that we have re-mashed the model, we can rerun the Inspector tool to clean up any residual errors. Click on Analysis and then the Inspector menu item. Click Auto Repair All, and inspector should repair any problems that still remain. When you're finished, click the Done button, as shown in Figure 23. Figure 23: Running the Inspector tool a second time Expose the cerebral vessels. We are now going to take an extra step and make a cut through the crowd of the skull to expose the cerebral vessels. This can be easily achieved in about one minute. First, make sure to select all the vertices in the model by hitting control-A or using the menus Select-> Modify-> Select all, as shown in Figure 24. The entire model should turn orange to indicate that it is selected. Figure 24: Selecting all the polygons in the model prior to performing a cut. Next, start a plane cut by choosing Select-> Edit-> Plane cut. The plane cut will show on the screen. The portion of the model that is transparent will be cut off. The portion of the model that is opaque will be left behind. Move the plane by using the purple and green arrow handles. Rotate the plane by using the red arc handle, as shown in Figure 25. Figure 25: Move and rotate the plane cut using the arrow and arc handles. In this case we wish to move the plane cut to the four head, and rotated 180° so that the transparent portion of the cut is at the top of the head, and the opaque portion encompasses the face, jaw, and lower part of the skull. After you have finished positioning the plane, your model should look similar to Figure 26. When you're happy with position, click Accept. Figure 26: The best position of the plane cut tool The crown of the skull will now be cut off, exposing the cerebral vessels within the brain. This includes the anterior, posterior, and middle cerebral arteries as well as the venous structures such as the straight sinus and sigmoid sinuses, as shown in Figure 27. As you can see, this is a highly detailed model and excellent for educational purposes and teaching neurovascular anatomy. Figure 27: The final model Conclusion In this tutorial we learn how to create a 3D printable skull and vascular model utilizing the free online service from embodi3D.com, as well as free desktop software 3D Slicer and Meshmixer. Both methods have their advantages and disadvantages. Embodi3D.com has a very fast and easy to use service. The desktop software is more difficult to use and learn, but gives more flexibility in terms of customization. Alternatively, you can use a combination of the two techniques, for example generating your model on the embodi3D.com website and then performing custom modifications, such as the plane cut we did in this tutorial, utilizing Meshmixer. I hope you found this tutorial helpful and entertaining. Please give the tutorial a like. If you are engaged in medical 3D printing, please consider sharing your work on the embodi3D.com website. Thank you very much and happy 3D printing!
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