cermep-bids-retro
lucie.chalet
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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.
Steps
cermep-bids-retro installation
Clone repository
In GitBash:
git clone https://gitlab.in2p3.fr/cermep/cermep-bids-retro.git
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
to the BIDS specifications to define all required tags for their modality.
Substeps below provide description and example for each column of the 3 input files.
This table must be filled in simultaneously with seq_overview.csv
This table is necessary for formatting of PET data, otherwise optional
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
