readme.md

Namer

entity_ux/ contains a web app to guide naming sequences as an alternative to this repo's ReproIn Creator Spreadsheet and includes entity and suffix requirements and description pulled from bidsschematools.

It's live on https://NPACore.github.io/reproin-namer (via github pages w/ doc/ symlink)

Resources

• ReproIn sequence name convention/standard
  • Siemens' scanner Dot Cockpit and Exam Card setup walk through (with screenshots)
  • automation implemented by heudiconv. See reproin.py
  • ReproIn Creator Spreadsheet: MRRC template to ReproIn using a formula with per column BIDS key-value pairs.
  • Flywheel Study Design Sheet (cf. gitlab template folder)
• goal is near automated BIDS Brain Imaging Data Structure conforming scanner dicom to nifti image+json sidecar name conversion.
  • Ideal for input in fmriprep
  • other BIDS apps
  • Flywheel gears.
  • and maybe (hopeful future) facilitate NIH share mandate compliance (cf. bids2nda)
  • for validation see bids-validator (nodejs)

Pipeline

1. 00_dcm-rewrite-from-xlsx.py rewrites (0018, 1030) Protocol Name using ReproIn conforming names in 7T-LunaSPA_ReproIn-SeqName.xlsx (see sheet w/equations on onedrive)
2. 01_dcm-bids.sh makes

bids/MRRC/SPA_Luna/20231103lunapilotspa2/sub-20231103lunapilotspa2/{anat,dwi,fmap,func}

with contents like

sub-20231103lunapilotspa2_acq-b0pfc_magnitude_dicom/
sub-20231103lunapilotspa2_acq-b0pfc_magnitude_heudiconv323_e1.nii.gz
sub-20231103lunapilotspa2_acq-b0pfc_magnitude_heudiconv323_e2.nii.gz
sub-20231103lunapilotspa2_acq-b0pfc_magnitude_heudiconv323_e3.nii.gz
sub-20231103lunapilotspa2_acq-b0pfc_magnitude_heudiconv323_e4.nii.gz
sub-20231103lunapilotspa2_acq-b0pfc_magnitude_heudiconv323_e5.nii.gz

See output-filelist.txt for full list.

Outputs

Makefile builds files in txt/

file	desc
input-orig.txt	original dicom headers per folder
input-repoin.txt	edited dicom headers using 7T-LunaSPA_ReproIn-SeqName.xlsx (00_dcm-rewrite-from-xlsx.py)
output-filelist.txt	heudiconv output: BIDS filelist
validate.txt	bids-validator output, using .bidsignore

Issues

• path SPA_Luna/20231103lunapilotspa2/sub-20231103lunapilotspa2 has redundant ID folder. Should be SPA_Luna/sub-20231103lunapilotspa2?
• Does not pass bids validation. see validate.txt.
  • multiple echos as e.g. _heudiconv323_e5 instead of _echo-5
  • no .json files!? (see missing in output-filelist.txt)
• how to encode session? only need in one sequence name?
• _dicom/ directoires are unwanted (but not a problem for Flywheel?). Ignored with .bidsignore

Dicom Notes

• 00_dcm-rewrite-from-xlsx.py edits Protocol Name and outputs to folders using Series Number.
• Study Description sets output folder using heudiconv --files: MRRC^SPA_Luna becomes bids/MRRC/SPA_Luna/

dicom header	example value
(0008, 1030) Study Description	LO: 'MRRC^SPA_Luna'
(0010, 0010) PAT Patient Name	LO: '20231103Luna_PilotSPA2'
(0010, 0020) Patient ID	LO: '20231103Luna_PilotSPA2
(0018, 1030) Protocol Name	LO: 'mtgre_noMT'
(0020, 0011) Series Number	IS: '48'