We first proceed to a calibration of DeepMReye (deepmreyecalib )and next next
evaluate it in condition of darkness and eye closed (deepmreyeclosed) This repository contain all code allowing us to analyse our dataset OpenNeuro:DSXXXXX.

Uriel LASCOMBES, Sina KLING, Guillaume MASSON, Matthias NAU, & Martin SZINTE

PyDeface; fMRIprep; FreeSurfer; FFmpeg; FSL; Inkscape; workbench

• Copy brain data from XNAT copy_data.py
• Copy behavioral data copy_data.py
• Deface participants t1w image deface_sbatch.py
  Note: run script for each subject separately.
• put eyetracking in latest BEP020 BIDS format
• Correct BIDS problems correct_bids_files.ipynb
• Validate bids format [https://bids-standard.github.io/bids-validator/] / alternately, use a docker [https://pypi.org/project/bids-validator/]
  Note: for the webpage, use FireFox and wait for at least 30 min, even if nothing seems to happen.

• fMRIprep with anat-only option fmriprep_sbatch.py
• Create sagital view video before manual edit sagital_view.py
• Manual edit of brain segmentation pial_edits.sh
• FreeSurfer with new brainmask manually edited freesurfer_pial.py
• Create sagital view video before after edit sagital_view.py
• Make cut in the brains for flattening cortex_cuts.sh
• Flatten the cut brains flatten_sbatch.py

• fMRIprep fmriprep_sbatch.py
• Load freesurfer and import subject in pycortex db freesurfer_import_pycortex.py
• High-pass, z-score, run correlations, average and leave-one-out average preproc_end_sbatch.py
• Make timeseries inter-run correlation maps with pycortex pycortex_corr_maps.py

• To make