We aim at assession gaze modulation of retinotopic areas in complete darknees.
This repository contain all codes allowing analysis of this preliminary dataset OpenNeuro:DS004271.

Margot CHEVILLARD, Tomas KNAPEN, Uriel LASCOMBES, Matthias NAU, Martin SZINTE

dcm2niix; PyDeface; fMRIprep; pRFpy; FreeSurfer; FFmpeg; FSL; Inkscape

Calib / GazeCW / GazeCCW: Resting-state task with different gaze direction change expLauncher.m
Calib / GazeLines / GazeColumns : Quick fixation change in complete darkness expLauncher.m
AttendFix_GazeCenterFS / AttendStime_GazeCenterFS : Retinotopy tasks expLauncher.m

• Copy pRF data from gaze_prf project and 3T anatomy.
• Copy event files from experiment code data to bids folder, rename sessions accordingly.
• Convert par rec to nifti and separate phase from bold using parrec_to_nii.py.
• Nordic correction in matlab using nordic_cor.m.
• Correct error in header of nordicized files
• Copy nordicized files in BIDS folder
• Create bold and epi .json files, as well as particpant.tsv and .json and dataset_description.json and readme
• Copy subject manually edited freesurfer segmentations
• BIDS validations: change header time unit and duration
• Deface subjects anatomy (to do in post-pilot study)

• run MRIQC using mriqc_sbatch.py
• run fMRIPrep (anat-only) 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

• run fMRIprep fmriprep_sbatch.py
• high-pass, z-score, average and leave-one-out average preproc_end.py
• Create pycortex database pycortex_import.py

• create the visual matrix design vdm_builder.py
• Execute prf_fit.py to fit pRF parameters: run only submit_fit_jobs.py
• Compute pRF derivatives compute_derivatives.py
  • add magnification factor see https://github.com/noahbenson/cortical-magnification-tutorial
• make pycortex maps pycortex_maps.py
• draw ROIs using Inkscape
• extract ROIs masks roi_masks.ipynb
• make pdf files with the maps pdf_maps.py
• make webgl with the pycortex dataset pycortex_maps.py
• send the files send_data.sh

• Execute cf_fit.py to fit CF and get projected PRF parameters: run only submit_fit_jobs.py
• make pycortex maps pycortex_maps.py

• extract all data as pickle files or tsv make_tsv.ipynb

• plot pRF parameters

  • lines_size_r2_ecc.ipynb
  • Violin_plot.ipynb
  • polar_angle.ipynb

• correlation maps between GazeCW/GazeCCW and GazeColumns/GazeLines using postproc/cormaps.py

• draw correlation maps on pycortex flatmaps using postproc/pycortex_cormaps.ipynb