MRRC Dicom Header Quality Assurance

Parse dicoms into a template database and alert on non-conforming sequences.

See

• make docs/ for building sphinx documentation
• locally in sphinx/index.rst)
• reference for restructured text sphinx docstrings
• make test for using doctests
• schema.sql for DB schema

TODO

• start at partial -- browser request, server send STATE
• don't throw error on null fields (calculate FoV, TA)
• remove data

Strategy

• build sqlite db of all acquisitions with subset of parameters
• use db summary to pull out "ideal template"
• check new sessions' acquisitions against template to alert via cron

#m  h  dom mon dow   command
30  0    *   *   *   /home/npac/src/mrrc-hdr-qa/02_update_db.sh

Notes

• "Sequence Name(0018,0024)" called "SequenceType" in taglist.txt is different per diffusion dcm (like ep_b5#1..ep_b1540#27)

• should look at n echos 0018,0086 and collapse across dicoms to make protocol mutliecho parameter

• precision changes between realtime streaming and offline dicom writes? see check_template.py

• inotify CREATE is catches files before they finish writing. Watch CLOSE_WRITE instead. Test slower write with smbclient

smbclient -U mrqart //localhost/dicomstream/ -c 'put 001_000001_000002.dcm sim/y.dcm'

MRQART

MR QA in Real Time (python port)

install

for start menu shortcut, copy bat shortcut into file into

%AppData%\Microsoft\Internet Explorer\Quick Launch\User Pinned\StartMenu

Developing

Use show_debug in a console to get a simdata textarea to send mock data.

TODO

• not red on null -- use mrqart computer files to test
• make systemctl service file
• rename input/template Current/Reference
• cron rm find -mtype +2 days and rm
• add help tooltips
• py motion affine -> FD and benchmark

Extensions/plugins

MRQART can be extended to support

• motion/framewise displacement (FD) measure reporting a la FIRRM
• dynamic EPI acquisition angle selection
• ntp (accurate) clock sync with trigger pulse (very limited analog to https://github.com/ReproNim/reprostim)

Prior Art

• mrQA
• sister project https://github.com/NPACore/mrqart/

Speed

exdcm=Resting-state_ME_476x504.14/MR.1.3.12.2.1107.5.2.43.167046.202208231445351851262117

hyperfine "./dcmmeta2tsv.py $exdcm" "./dcmmeta2tsv.bash $exdcm" 

Benchmark 1: ./dcmmeta2tsv.py Resting-state_ME_476x504.14/MR.1.3.12.2.1107.5.2.43.167046.202208231445351851262117
  Time (mean ± σ):     952.2 ms ±  37.4 ms    [User: 559.1 ms, System: 86.9 ms]
  Range (min … max):   876.5 ms … 1014.5 ms    10 runs
 
Benchmark 2: ./dcmmeta2tsv.bash Resting-state_ME_476x504.14/MR.1.3.12.2.1107.5.2.43.167046.202208231445351851262117
  Time (mean ± σ):     822.5 ms ±  69.3 ms    [User: 73.3 ms, System: 51.0 ms]
  Range (min … max):   703.1 ms … 896.1 ms    10 runs
 
Summary
  ./dcmmeta2tsv.bash Resting-state_ME_476x504.14/MR.1.3.12.2.1107.5.2.43.167046.202208231445351851262117 ran
    1.16 ± 0.11 times faster than ./dcmmeta2tsv.py Resting-state_ME_476x504.14/MR.1.3.12.2.1107.5.2.43.167046.202208231445351851262117