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OHBM 2019 Hack-a-thon (Done)

added exception for checking existence of subjects directory, had to move to end of parse opts to allow -sd input to propagate

moved exception for report dir to end of parse opts

reorganized files (clean up) and created parent call function 'surfergem'

added dependency checks for parallel, freesurfer

checked status and manifest functions (works!)

checked statistics summary (works!)

added improved option parsing for the --web-report opt, now checks to make sure that argument following option is not another option i.e) '-' prefix and sets default SUBJECT list to those with 'done' status

added single subject processing for subject-edits

fixed bug with checking if input subject id matches existing subject in subjects_dir

fixed bug with printing landing pages and nested tiles

PRIMARY TODO

x use nilearn write to html function to get surfaces working in html x extract and embed surface morphometrics to html x compile edits and project to surface x group average functions x --> average template (make_average_subject) x --> average morphometrics, edits, snr on surface Once primary done: Update repository with done, need to update documentation and release to community

SECONDARY TODO

  • rerun failed jobs
  • add time started in SGE for status output
  • exception check - does recon-all.log exist?
  • think about how to show contrast to noise ratio x should ANTs be added as a dependency? x --> maybe individual binaries can be compiled as dependencies
  •   --> DenoiseImage noise estimation for SNR maps
  • update documentation with java dependency
  • add parsing of participant metadata (bids standard participants.tsv?)