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gre-1dnav-analysis

Analysis pipeline for FFE 1d retrospective navigator correction for spinal cord imaging on Philips scanners.

1 - Download data

See: https://openneuro.org/datasets/ds006347/download

Some notes about the data:

  • Contrast: _T2starw
  • Varying number of sessions across participants: ses-01, ses-02, etc.
  • With | without navigator: *_rec-navigated | *_rec-standard
  • Varying location: acq-lowerT | acq-upperT | acq-LSE

2 - Run data analysis scripts

2.1 - Clone the repository and navigate to the script directory

git clone https://github.com/sct-pipeline/gre-1dnav-analysis.git
cd <PATH_TO_CLONED_REPOSITORY>

Note

Please make sure to replace <PATH_TO_CLONED_REPOSITORY> with the full path to the folder where the repository has been cloned

2.2 - Execute the data processing script for all subjects

sct_run_batch -script process_data.sh -path-data <PATH_TO_DATA> -path-output <PATH_TO_OUTPUT>

Example:

sct_run_batch -script process_data.sh -path-data ~/data/ds006347/ -path-output ~/temp/ds006347_20250612_144520

3 - Run figure scripts

Warning

TODO