2016 Winter Project Week/Projects/SlicerCMFNextSteps

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In the Dental and Craniofacial Bionetwork for Image Analysis we bring together clinical dental researchers, computer scientists and engineers from NA-MIC, to address the following gaps between clinical choices and effective treatments in dentistry: (a) a lack of quantitative imaging biomarkers of bone structure; (b) limitations in techniques to assess treatment effects and quantify degradation or repair of bone; (c) a lack of software and training for the use in dental clinical practice management.

We work to integrate and share imaging quantitative methodology in Dentistry, supporting patient-specific decision making and assessment of the disease progression via registration of serial images. We have developed SlicerCMF (Craniomaxillo facial Slicer) including only computational algorithms that provides open source dental image analysis to 3DSlicer users.

Our long-term goals are to aid the decision process of treatment procedures, allow translation of basic science developments into the clinical field with efficient engineering solutions, and train both young clinical image specialists and experienced clinical researchers on the new tools and techniques.

This work is being supported by the National Institute of Dental & Craniofacial Research and the National Institute of Biomedical Imaging and Bioengineering under Award Number R01DE024450.

Key Investigators

https://sites.google.com/a/umich.edu/dentistry-image-computing/Personnel

  • Lucia Cevidanes: University of Michigan. Department of Pediatric and Orthodontic Dentistry.
  • Beatriz Paniagua: University of North Carolina at Chapel Hill. Departments of Psychiatry, Computer Science and Orthodontics.
  • Steve Pieper: Isomics, Inc.
  • Juan Carlos Prieto: University of North Carolina at Chapel Hill. Department of Psychiatry.

Project Description

Objective Approach and Plan Progress and Next Steps
  • Reflect on the past projects/extensions we have done for SlicerCMF during the SlicerExtensions Breakout session
  • Plan and design next steps in our SlicerCMF projects.
  • Clear idea on what are the important points in our steps forward:
  1. In order to be able to integrate our imaging results with other biomarkers collected, we need a more streamlined way to represent and store our data.
  2. Great inspiration from the QIICR project: Work items to adopt the DICOM standard, create new snowmed terminology for CMF and new structured report fitting our research data.
  3. Chronicle as our storage system.
  4. New data collection from existing funds from UMich and Bea's R21.
  • We will work on drafting aims before March, to bounce ideas with the PO's at AADR2016. Aim1 and Aim2 clinical, Aim3 will be about creating a data standard, data storage and data query system.
  • Timeline:
  1. First submission of project in July 2016.
  2. New interns (arriving July 2016) will wrap up current modules and development work, and work in preliminary data for the grant.
  3. First score in October 2016.
  4. Resubmission in February 2016 with further preliminary data.
  • Work items:
  1. Lucia: draft clinical aims.
  2. Bea: gather ideas from this meeting and communicate via email with Steve.
  3. Steve: task list for preliminary work.

Background and References

Ideas and Minutes of meetings

Tuesday, January 5th 2016

  • Slicer extension breakout session: Talks about creating an standard for data gathering. Talks about workflows and batch processing.
  • Andrey and Ron think its possibly interesting to adopt the DICOM standard as data objects for the database of the grant.

Wednesday, January 6th 2016

  • Interesting discussions about persistence of data across modules in the Slicer extension breakout session
  • Talks with Ron and Andrey about benefiting about the QIICR work.
  • Talking with Steve Pieper about aims, sketch aims, is there anybody doing DICOM cephalometric standards (look for Dave Altobelly - 1993).
  • Look at FaceBase project.
  • DICOM Michael Onke-- and DCMTK group
  • Structured reports in DICOM - Snowmed CT terminology is brought up into the DICOM standard
  • QIICR Breakout session:

Imaging biomarkers is a great buzzword in our community. Different quantitative measurements, but none of them are imaging. Different biomarkers are being created but only few are applied to the clinic. Studies are not reproducible, its difficult to reproduce results, new environment is needed. Open source analysis tools, use standards to exchange results etc. Provide open source informatics infrastructure to support development of quantitative imaging biomarker analysis tools and standardize data sharing. DICOM has been changing to reflect the needs of the research community. DICOM annotations: with a lot of possibilities for different data. DICOM can encode different information, and you can use tools for displaying human readable data. Main idea is to store data in DICOM format but use other research formats for analysis (including nrrd) and it is important to have converters. Tools for DICOM conversion back and forth other formats.

TCIA has all the identification and anonymization. CTP standard. Their project does not take care of it. We need to think what to do with it.

Thursday, January 7th 2016

  • DCBIA organizing work with Lucia.