Namer

entity_ux/ contains a web app to guide naming sequences.

It's live on https://NPACore.github.io/reproin-namer (via github pages w/ doc/ symlink). The release zip also contains the static assets needed to view locally and offline.

ReproIn Creator Spreadsheet is an alternative. Both the web app and sheet include entity and suffix requirements and description pulled from bidsschematools.

Local and Offline

The web app also on https://npacore.github.io/reproin-namer can be used locally.

# from relase
unzip -d reproin-namer release_1.0.0.zip
firefox reproin-namer/index.html

# from git
git clone https://github.com/NPACore/reproin-namer
cd reproin-namer/entity_ux
firefox index.html

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)

Testing names

Consistant naming is not an end in itself! We also want to confirm ReproIn names can easily be moved to BIDS. To that end, this repo also hosts scripts that can update DICOM headers and test the BIDS naming piepline.

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'