Oct 11, 2023
Version 1
cermep-bids-retro V.1
- lucie.chalet 1,2
- 1CarMeN Laboratory, Université Claude Bernard Lyon 1, INSERM U1060, INRA U1397, Lyon, France;
- 2Olea Medical, La Ciotat, France
Protocol Citation: lucie.chalet 2023. cermep-bids-retro. protocols.io https://dx.doi.org/10.17504/protocols.io.261ge319dl47/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 22, 2023
Last Modified: October 11, 2023
Protocol Integer ID: 79230
Keywords: mri data to bids standard, mri data, bids standard, formatting of retrospective pet, dicom database, advanced data quality assessment, bids guideline, following bids guideline, data, flexible method for bid, bid, numerous metadata, dicom tag, retrospective pet, lacking dicom tag, input csv file, retro cermep, database, cermep, acquisition
Funders Acknowledgements:
ANR CYCLOPS
Grant ID: ANR-15-CE17-0020
ANR CMRO2
Grant ID: ANR-21-CE17-0028
RHU MARVELOUS
Grant ID: ANR-16-RHUS-0009
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Abstract
cermep-bids-retro enables the formatting of retrospective PET and MRI data to BIDS standards from DICOM databases. When dealing with pre-clinical imaging modalities, numerous metadata are overlooked during acquisitions making it difficult to automatically format following BIDS guidelines. This python-based project is a flexible method for BIDS formatting with input csv files to compensate for lacking DICOM tags. And advanced data quality assessment.
cermep-bids-retro installation
Create conda environment
cd cermep-bids-retro
conda env create -f environment.yml
conda activate bids-retro
Fill-in input files
This step is key to a functional method. It requires a good knowledge
of the available tags and fields in the DICOM data and one can always refer
Substeps below provide description and example for each column of the 3 input files.
Description and examples to fill in seq_overview.csv
This table must be filled in simultaneously with seq_overview.csv
Desciption and examples to fill in dcm2bids_tags.csv.
This table is necessary for formatting of PET data, otherwise optional
Description and examples to fill in pet_doses.csv
Run formatting task
Replace argument values and run task from command line:
python bids_retro\\main.py \
--src_mri "path\to\modality" \
--src_pet "E:\PhD\temp\data_fabien\raw_dcm" \
--sequences_overview "inputs\seq_overview.csv" \
--pet_doses "inputs\pet_doses.csv" \
--dcm2bids_tags "inputs\dcm2bids_tags.csv" \
--species "name of species" \
--src_structure "A" \
--in_sub_dcm_list "subjectA,subjectB" \
--in_ses_dcm_list "session" \
--dest "path\to\bids\formatted\destination" \
--quality_testing 1 \
--results "path\to\save\quality_analysis\results" \
--include_dicom 0 --verbose 1