BeaProjectsPage2016

Craniofacial

• Location of all craniofacial in the NIRAL servers: /projects5/CMF
• Location of craniofacial archive: /athena_archive/NIRAL/projects5

Cevidanes pre-R01

• Purpose of this study: Study TMJ OA using imaging biomarker. Multiple studies involving different stages of the disease and symptoms. Plenty of shape analysis results involving TMJ condyles. This work paved the way for our TMJ OA R01 submission in Feb-2012, funded in Sept-2013 (see below) PI-Cevidanes.
• Published: Plenty http://www.ncbi.nlm.nih.gov/pubmed/?term=cevidanes+temporomandibular
• Status: Finished.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/OACevidanes_2009-2013_July2016.tar.gz

TMJ R01

Summary: This work was supported by the National Institute of Dental & Craniofacial Research and the National Institute of Biomedical Imaging and Bioengineering under Award Number R01DE024450. Funding period September-2013 to August-2017. PI - Cevidanes/Paniagua.

Status: Ongoing.

Contents:

• Archive: Discontinued tests and other experiments.
• CTvsCBCT: This project is finished. It is part of the validation part of aim 1 in the grant that compares CBCT to CT. Simple analysis using shape correspondence.
• Workshop_IADR2015: This is an example folder that contains the tools and data for our workshop in 2015. This is before SlicerCMF.
• DiagnosticIndex: Ongoing research for Aim 1. Nothing should be needed to be continued from here, since the last experiments were performed by Bea and published in SPIE2017. This project is at a good point for moving onto something new.
  • PilotData_MatlabWork: Experiments with DWD performed by Bryan Jung in 2012-2014. Mostly matlab scripts developed by Steve Marron.
  • newSPHARMtests_tiltedData_SSMMethod: These are some spharm experiments seeing the performance of the method published in Shape2015 and SPIE2017 with tilted data.
  • LookUpTables: csv files with group classification for all the different combination of subgroups that Lucia and her team created.
  • Code_Bea_JP: Bea's code using SSM. JP's code implementing PNS using C++.
  • Data:
    • Both: All control + OA cases.
    • Both_noG2: All control + OA cases (minus overgrowth group)
    • ControlGroup: Control Group
    • Larger_crop: same dataset cropped lower in the condylar neck.
    • OA: All OA cases.
    • Old_Chronic_Initial_Control: Initial grouping of dataset including Control + OAInitialDiagnosis
    • Grouping: Grouping work, initial 7 clinical subgroups.
    • Visualization[...]: These folders contain recostructions of the datasets, named in a certain order to be visualized in paraview as a video.

Texture analysis

• Purpose of this study: Evaluate TMJ OA subchondral bone texture using texture analysis methods. PI-Paniagua. Submitted as R21, still maybe funded.
• Published: http://www.ncbi.nlm.nih.gov/pubmed/26085710
• Status: Transferring.
• This project stays in NIRAL servers. Archiving status TBD.

TMJSimulation

• Purpose of this study: Study the general performance of radiologists on diagnosing TMJ OA using only multiplanar evaluation of CBCT condyles. Simulated defects were generated in a collection of TMJ healthy condyles of known location and depth. PI-Nguyen-Paniagua.
• Published: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4518713/
• Status: Finished.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/TMJSimulation_July2016.tar.gz

MRI - Nguyen

• Purpose of this study: Pilot work prior grant submission. Using MR to generate a TMJ complex model. PI-Nguyen-Paniagua.
• Published: N/A
• Status: Ongoing.
• This project is located at: /projects5/CMF/MRI-Tung

BSSO - Nguyen

• Purpose of this study: To introduce new 3-D imaging techniques to characterize shape and volume changes of the oropharyngeal space after bilateral sagittal split osteotomy (BSSO) advancement. PI-Nguyen-Paniagua.
• Published: http://www.ncbi.nlm.nih.gov/pubmed/27138685 (2016)
• Status: Finished.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/BSSO-Tung-Paniagua_July2016.tar.gz

Condylar tork

• Purpose of this study: To test mandibular condyle tork after orthognathic surgery. PI-Nguyen.
• Published: unpublished.
• Status: discontinued.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/CondylarTork_July2016.tar.gz

WUSTL - Craniosynostosis

• Purpose of this study: Pilot work studying brain structure of sagittal craniosynostosis in MRI. Using MR to generate a TMJ complex model. PI-Paniagua/Patel.
• Published: Submitted to SPIE2017.
• Status: Transferring (TBD).
• This project is located at: /projects5/CMF/Craniofacial/WUSTL_Craniosynostosis

vanAalst - Craniosynostosis

• Purpose of this study: Study craniofacial features of sagittal and metopic craniosynostosis using medical CT as input data. Trying to generate pilot data for an R21 submission (submitted February 2013, unfunded and not resubmitted). PI-vanAalst (no longer at UNC)
• Published: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898845/
• Status: discontinued.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/CraniosynostosisPilot_July2016.tar.gz

vanAalst - Plastic_Surgery

• Purpose of this study: A miscellaneous collection of projects and studies carried out by interns and fellows from Dr. van Aalst laboratory. PI in the NIRAL - Paniagua.
• Published: not to my knowledge. Maybe to clinical conferences.
• Status: discontinued.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/PlasticSurgery_vanAalst2012-2013_July2016.tar.gz

Healthy Brain Shape

• Purpose of this study: Creation of normative databases of healthy (full) brain shape. Sources IBIS and CONTE samples. Contains SPHARM correspondent meshes as well as 4D atlases of normative growth (Gerig/Fishbaugh regression). PI-Paniagua.
• Published: Part of the work also submitted to SPIE2017.
• Status: Ongoing.
• This project is located at: /projects5/CMF/Craniofacial/Brain_Shape

SBIR - Kitware

• Purpose of this study: To develop intra-operative visualization techniques that incorporate freehand ultrasound imaging technology and 3-D image registration techniques to assist oral maxillofacial surgeons.
• Published: AECAI 2015 workshop.
• Status: finished.
• This project has been archived in Athena: athena.ia.unc.edu: /athena_archive/NIRAL/projects5/CMF/SBIR-SurgicalSimulation_July2016.tar.gz

This work was supported by the National Institute of Dental & Craniofacial Research Award Number R43DE024334. Funding period August-2014 to July-2016. PI - Enquobahrie/Nguyen.

Tools

• This folder includes scripts to build SlicerCMF.

Instructions on how to build:

1. Download and install the last Nightly. This is specially important if SlicerCMF has to contain extensions that require the last changes in Slicer trunk.
2. Download and install a python Slicer module named CustomSlicerGenerator https://github.com/pieper/CustomSlicerGenerator Installation involves adding the path of the CustomSlicerGenerator to Slicer (the nightly you just downloaded) manually, via Edit >> ApplicationSettings >> Modules >> AddPath.
3. Write a json file that describes what modules and extensions to package in SlicerCMF. (example:
4. Run the CustomSlicerGenerator module in Slicer. Its pretty easy, just specify the output folder for the package and the input Json file.
5. Very important, try that all extensions and modules work.

Status: Ongoing.

Contents of files in Athena Archive (prior July 2016)

-rw-r--r--. 1 jblocher res 281274135 Nov 24 2014 Airways_Nov2014.tar.gz

This project looked at Shape Analysis of airways. PI-Cevidanes/Nguyen. Discontinued and unpublished.

-rw-r--r--. 1 jblocher res 508048609 Nov 24 2014 BoneAnchors_Nov2014.tar.gz

This project looked at the use of Herbs distraction correction for Class II children. PI-Cevidanes/Nguyen/DeClerk. Discontinued. http://www.ncbi.nlm.nih.gov/pubmed/22748987 http://www.ncbi.nlm.nih.gov/pubmed/21055597 http://www.ncbi.nlm.nih.gov/pubmed/21055597 http://www.ncbi.nlm.nih.gov/pubmed/19577154

-rw-r--r--. 1 jblocher res 1146101760 Nov 24 2014 HeidiPhD_Nov2014.tar.gz

Initial work for Heidi Kohltfarber's Phd. Discontinued and unpublished.

-rw-r--r--. 1 jblocher res 412221660 Nov 24 2014 MandDistraction_Nov2014.tar.gz

Initial work for visiting scholar to the Cevidanes lab from Turkey in 2009. Discontinued. Publication status unknown.

-rw-r--r--. 1 jblocher res 9737915817 Nov 24 2014 PrePostSurg_Nov2014.tar.gz

Work for the Stability grant. Funded project by the National Institute for Dental and Craniofacial Research, Award number R01 DE005215. PI-Proffit/Phillips. Funded period 1979-2013. Discontinued. Plenty of publications: https://projectreporter.nih.gov/project_info_results.cfm?aid=8436285&icde=30424210

-rw-r--r--. 1 jblocher res 224147141 Nov 24 2014 SoftTissue_Nov2014.tar.gz

Pilot work for soft tissue shape analysis. PI-Cevidanes. Discontinued and unpublished.

-rw-r--r--. 1 root root 46393159877 Nov 25 2014 Asymmetry_Nov2014.gtz

Abeer Alhadidi's Ms and PhD image processing work. PI-Cevidanes/Paniagua. Publications: http://www.ncbi.nlm.nih.gov/pubmed/?term=alhadidi+asymmetry

Miscelaneous

NIRAL virtual machines

In venus, there is an venus.ia.unc.edu:/opt/Bea/VB folder that contains the virtual machines and the images for the NIRAL system tools dated to 2013. Feel free to delete this if this is not useful for you any longer.

Work and Home folders

They have been cleaned up and downsized to the minimum. /home/paniagub /work/paniagua

Lateral Ventricle Shape Analysis

Experiments evaluating the last version of the results can be found @ /Human/conte_projects/CONTE_NEO/Data/Vent_Shape/LastVersionPaper_July2016 This folder contains:

• The last version of the paper that Sarah and Bea worked on. NeuroImage_LV_Shape_4-28-2016.docx.
• Figures: High Resolution figures that the last version of the paper contained.
• Final_Results_Hongtu: VTK files (averages) with all the different color maps embedded as scalar maps.
• Excel file with volumetric data analysis from hongtu, including graphs and figures: Summary_02232016.xls

Rodent

See Bea Rodent Project Pages July-2016