NBE-E453001 - Special Course in Human Neuroscience V D: Imaging Brain Microstructure and Connectivity with Diffusion MRI, Lectures, 23.4.2024-7.6.2024

Topic outline

• Select topic General

  General
  • Select activity Announcements

    

    Announcements Forum
  • Select activity Session 1 slides

    

    Session 1 slides File PPTX
  • Select activity Self-study before Session 2 and homework submission (DL 28.4. at 23:59)

    

    Self-study before Session 2 and homework submission (DL 28.4. at 23:59) Assignment
  • Select activity Session 2 basic preprocessing commands

    

    Session 2 basic preprocessing commands File SH
  • Select activity Session 2 slides

    

    Session 2 slides File PPTX
  • Select activity Self-study before session 3 + submit learning log about session 2 (DL 13.5. 23:59)

    

    Self-study before session 3 + submit learning log about session 2 (DL 13.5. 23:59) Assignment
  • Select activity MRtrix3 built for linux

    

    MRtrix3 built for linux File ZIP

    This can be unpacked to e.g. your home folder on vdi.aalto.fi. In addition, the following line needs to be added to the end of the .bashrc file:

    export PATH="$home/mrtrix3/bin:$PATH"

    Replace $home with the output of pwd command when in your home folder, for instance:

    pwd

    /u/72/tjroine/unix

    
    

  • Select activity Return the 1st draft of project work report (DL 20.5. 23:59)

    

    Return the 1st draft of project work report (DL 20.5. 23:59) Forum

    Please submit here the 1st draft of the project work report. Please create a new discussion topic for each group, so the peer-review comments can be easily organized. 

    The draft should include a Background section (approx. 1-1.5 pages) with a literature review (incl. citations), and concrete aims of the project, and a Methods section (approx. 0.5-1 pages) with a short description of the methods you will use. It is not required to have results or images at this stage but you may of course proceed further and include them. Total recommended length of the project report is 6 pages including also a Results section with figures and tables, a Discussion section with reflection about the results, their significance, and the suitability of the selected methods, and a list of references.

  • Select activity Learning log for session 3 (due 20.5.2024 at 23:59)

    

    Learning log for session 3 (due 20.5.2024 at 23:59) Assignment
  • Select activity Diffusion tensor imaging slides

    

    Diffusion tensor imaging slides File PDF
  • Select activity Submit learning log 4 and peer-feedback to the forum (deadline 29th May)

    

    Submit learning log 4 and peer-feedback to the forum (deadline 29th May) Assignment
  • Select activity Session 4 slides

    

    Session 4 slides File PDF
  • Select activity Session 5 - Connectivity networks and microstructural modeling

    

    Session 5 - Connectivity networks and microstructural modeling Lesson

    As a preassignment before the next session (Thursday 30.5.), please watch:

    
    

    From 44mins until the end --> 
    

    
    

    and read:

    Graph theoretical analysis: https://www.nature.com/articles/nrn2575

    Microstructural modeling: https://www.sciencedirect.com/science/article/pii/S0165027020302843

    and give a brief look to:

    the NEXI model: https://www.sciencedirect.com/science/article/pii/S1053811922003986

    and to the fixel-based analysis pipeline: https://www.sciencedirect.com/science/article/pii/S1053811921006923

  • Select activity MRtrix3 build without GUI (works on cluster)

    

    MRtrix3 build without GUI (works on cluster) File ZIP
  • Select activity Submission of learning log and project work report (DL 10.6.2024)

    

    Submission of learning log and project work report (DL 10.6.2024) Assignment

    Please submit the last learning logs and project work reports (one submission of the project work report per group is enough) here by Monday evening (10 June 2024).

  • Select activity Lecture notes Session 5

    

    Lecture notes Session 5 File PDF