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MRRC Prisma Phantom QC

Program/QC.m input/QA_PRISMA3QA_20240809_180204_160000/EP2D_BOLD_P2_S2_5MIN_0003/ outputs/

jq .snrpk < outputs/stats.json # 242.8687622000182
ls outputs/bars.png

TODO

  • resolve fw-beta gear install error

    Error: writing blob: determining upload URL: http: no Location header in response

  • break up Program/dostat.m and add tests using input/trunc
    • optimize/vectorize esp. std command? surprisingly slow
    • profile against matlab runtime - switch to ML compiled version if octave is much slow
  • slim docker container: build octave without Xorg or java (likely to be useful for other containers later)
  • add subset of stats.json to FW DB
  • create script (outside of flywheel) to plot stats across time

Testing

make test
make test-docker

Using octave %!test in-file tests. See bottom of Program/readshimvalues.m.

Editiing

  • Makefile guides through steps
  • see .docker then .gear for packaging

  • mess of other files for .gear-run.txt with various input files setup (download input zip and setup config.json)

    • fw-beta is used for gear setup
    • this started from hello-world gear
    • Program/run.py still used for flywheel entry (sets up input/ and output, eventually handles DB)

  • bump version in manifest.json: "version": and "custom": { "gear-builder": { "image": "npac/mrrcqa:1.0.20240822" } } current match.

Noteworth files

file desc
Program/QC.m octave script, docker entrypoint into @chms matlab QC code
Program/run.py flywheel-aware entrypoint for gear. unzips and dispatches to QC.m
Makefile make interface to building and testing recipes
Dockerfile describes software dependencies, recipe for container
config.json fw-beta gear run input. built with Makefile

Interfacing with Flywheel

  • repo init with copy from https://gitlab.com/flywheel-io/scientific-solutions/tutorials/Gear-Building-Tutorial/-/tree/hello-world

  • for archive as file type in manifest.json, see https://docs.flywheel.io/User_Guides/user_file_types_in_flywheel/ (c.f nifti)

  • clasification qa picked form list on https://flywheel-io.gitlab.io/tools/app/cli/fw-beta/gear/upload/

Phantom