TUD SS20 tractography Team's diary
Zihan Zhang KW21: Initial Literature review on colormap. KW22: Literature review on topics: DTI, MRI, and Tractography KW23: Install and explore CGV framework and familiarize with the code. KW24: Review on colormap by Kenneth Moreland et al. KW25: Implement colormap data of Blackbody and Extended blackbody. Preparation of slides for presentation and the speech. KW26: Explore and install FSL software and take the course. Install MRIcron and MRIcroGL to get NIFTI file format from DICOM. KW27: Familiarize with Diffusion MRI and do FA and MD calculation by FDT. KW28: Install 3D slicer to get data details. Compare TRK file with NIFTI file to get the connection. KW29: Implement volume rendering on DGV framework. Upload to github. KW30: Fix dimension conversion and Eliminate invalid data to improve rendering accuracy. Upload to github. KW31: Write report.(implement chapter) KW32-33: Edit report and Provide images to support evaluation part.
Alaleh Kamel
KW20: General research on tractography and dMRI.
KW21: Initial literature review on color mapping. Tried to install CGV on Mac. Tried to understand the details of the “Measuring the Effects of Scalar and Spherical Colormaps on Ensembles of DMRI Tubes” paper.
KW22: Further work on installing CGV using VMWare on Mac: unsuccessful. The decision was that Mac users do more on the non-CGV part.
KW23: Tried to familiarize myself with mathematical concepts of Boy’s surface method (paper: Coloring 3D Line Fields Using Boy’s Real Projective Plane Immersion)
KW24: Contact the authors of the Boy’s Surface paper to get exact the coefficients and functions they had used. Implemented the boy’s surface color mapping in C++ outside CGV. Helped with integrate it in CGV.
KW25: Preparation of the intermediate presentation and slides. implementation of Boy’s surface method and Absolute Value method in MATLAB to generate some images.
KW26: Tried to understand the concepts of new tasks. Tried to install FSL software.
KW27: No work on team project due to Seminar presentation.
KW28-29: It was decided that I prepare the questionnaire so that teammate can implement it in CGV. Started the work on the questionnaire, trying to understand the design method, objectives, etc.
KW30: (chickenpox)
KW31: Designed the Questionnaire and uploaded it on GitHub. Discussions in the team to see what questions we can actually implemented. Started research on similar papers to find out more ideas about it. Tryied to design questions with minimum 3D rendering requirements.
KW32: Finally decided that only one question can be implemented. Carried out the questionnaire using the photos that Zihan had sent. Started writing the evaluation part of the report.
KW33: Evaluation of the results, statistics, and trying to justify them. Editing and revision of the group report, match the parts in LaTex and uploaded on GitHub.
Yu Kong KW21: Get basic knowledge of DMRI, tract data. KW22: Literature review on scalar colormap/Install CGV framework but fail/ Try to understand codes. KW23: Still trying to install CGV framework with Susu’s help, still fail/ Read papers of spherical colormap. KW24: Give up installing CGV and write codes of scalar colormap, Susu helps to test. KW25: Prepare for intermediate presentation. KW26: Get basic idea of FA and MD with FSL. KW27: Compute FA and MD/ Install 3D slicer. KW28: Have meeting with Susu& Zihan for codes of reading Nifti files with LAYNII. Since I have no CGV framework we work together in the classroom. KW29: Have meeting with Susu& Zihan, implement the FA and MD with colormaps with the help of David. KW30: Divide work for report. Prepare papers and result screenshots. Discuss the evaluation part. KW31: No work. KW32-33: write report Chapter 1 introduction, Chapter 2 scalar colormap& spherical colormap
Susu Hu
KW19:
• First meeting together
• Get familiar with the task
KW20:
• Reading paper, trying to understand six scalar maps and four spherical color maps
• Trying to install CGV framework
KW21:
• Successfully installed CGV framework
• Getting familiar with CGV framework functions
• Starting to implement cool-warm colormap
KW22:
• Cool-warm colormap implemented
• Starting to work on diverging color map
KW23:
• Extended Kindlmann colormap implemented
KW24:
• Read the paper further to understand the process of localization and comparison survey
• Start working on the intermediate presentation
• Help others implemented their colormapping in CGV framework
KW25:
• intermediate presentation rehearsal
• finish intermediate presentation slides
KW26:
• intermediate presentation
• FA calculation added after the presentation
KW27:
• Download and install FLS, calculation FA using TBSS
KW28:
• Calculating FA, MD
• Load nii file to CGV frame
KW29:
• Matching .nii file and .trk file with corresponding positions
• Apply FA/MD to color mapping
KW30,31:
• Pause due to teamate's illness
KW32:
• Write the report and help Alaleh to design the survey and
KW33:
• Finish the report