Week 1

Overview

  • Spent time familiarizing myself with software and tools that are used in sensein lab (e.g., datalad) and mcgovern (openmind)
  • Explored datasets and applied for access to NIMH, UK Biobank, and CHOP. Talked with Hoda about UK Biobank, will meet in person soon. Need to contact Steve and/or Debbie (have not met them yet). Available info on UK Biobank and ABCD is pretty comprehensive, need more details about CHOP (will know more when I get access).
  • Have been reading the precision medicine literature, familiarizing myself more with recent developments in the field
  • Plan on compiling a set of papers relating to neuroethics that I think will be pertinent to future projects (especially CHOP-related project)

Software/Tools

  • Datalad
    • how many datasets are currently hosted on datalad?
  • Openmind
    • got an account + took the course. I’ve used slurm a lot previously (used savio cluster at berkeley and I’m familiar with submitting jobs, running bash scripts etc.
  • Singularity
    • are there any general-use singularity containers on openmind for common neuroimaging preprocessing? (fMRIPrep, freesurfer etc.)
  • conda
  • Reproschema

Project Ideas