Authors (alphabetic order):

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Marco BEDINI, Sina KLING, Uriel LASCOMBES, Martin SZINTE

Environment Set Up

To install dependencies run the following: pip install -r requirements.txt Afterwards we recommend working with a conda environment.

Install pycortex:

CFLAGS="-std=c99" pip install git+https://github.com/gallantlab/pycortex.git

Install prfpy:

git clone https://github.com/VU-Cog-Sci/prfpy.git

cd to folder

python installer.py everything should be fine, so to check that all version are correct: pip install -r requirements.txt

Task-specific analysis

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After pRF analysis each project has its own analysis. The project's read me can be found at :

• RetinoMaps README.md
• Amblyo_prf README.md
• Amblyo7T_prf README.md
• centbids README.md

Main behavioral, structural MRI and functional MRI analysis

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BIDS

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• Deface participants t1w image deface_sbatch.py
• BIDS eyetracking conversion run_eye2bids.py
• Validate bids format [https://bids-standard.github.io/bids-validator/] / alternately, use a docker [https://pypi.org/project/bids-validator/]
• Generate experimental design matrix create_design_matrix.py

MRI Data analysis

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Individual analysis

Analyses are run on individual participant (sub-0X) surface (fsnative) or their projection on the HCP cifti format (170k).

Structural preprocessing

• fMRIprep with anat-only option fmriprep_sbatch.py
• Create sagittal 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 sagittal 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

Functional preprocessing

• fMRIprep fmriprep_sbatch.py
• Load freesurfer and import subject in pycortex db freesurfer_import_pycortex.py
• High-pass, z-score, average and leave-one-out average preproc_end_sbatch.py

Functional postprocessing

Analyses are run on individual participant (sub-0X) surface (fsnative) or their projection on the HCP cifti format (170k).

Inter-run correlations

• Compute inter-run correlation compute_run_corr_sbatch
• Make inter-run correlations maps with pycortex pycortex_maps_run_corr.py or pycortex_maps_run_corr.sh

PRF Gaussian fit

• Create the visual matrix design vdm_builder.py
• Run pRF gaussian grid fit prf_submit_gridfit_jobs.py
• Compute pRF gaussian grid fit derivatives compute_gauss_gridfit_derivatives.py
• Make pRF maps with pycortex pycortex_maps_gridfit.py or pycortex_maps_gridfit.sh

PRF ROIs

• Create 170k MMP rois create_hcp_rois.ipynb or copy sub-170k in pycortex folder from Retinomaps.
• Create 170k MMP rois masks create_mmp_rois_atlas.py
• Draw individual ROI on fsnative data using Inkscape
• Make ROIS files make_rois_img.py
• Create flatmaps of ROIs pycortex_maps_rois.py or pycortex_maps_rois.sh

PRF CSS fit

• CSS fit within the ROIs prf_submit_css_jobs.py
• Compute CSS statistics css_stats_sbatch.py
• Compute CSS fit derivatives compute_css_derivatives.py
• Compute CSS population cortical magnification (CM) css_pcm_sbatch.py
• Make CSS pRF fit derivatives and CM maps with pycortex pycortex_maps_css.py or pycortex_maps_css.sh
• Make general TSV with CSS pRF fit derivatives, statistics and CM make_tsv_css.py
• Make ROIs figure specific TSV with CSS pRF fit derivatives, statistics and CM make_rois_fig_tsv.py or make_rois_fig_tsv.sh
• Make ROIs figure of CSS pRF fit derivatives, statistics and CM make_rois_fig.py or make_rois_fig.sh
• Merge all figures merge_fig_css.py

Group analysis

We run either analysis on the template of the HCP cifti format (sub-170k) in which individual results are averaged on a template
or we ran an ROI-based group analysis determined individually on subject surfaces fsnative (group).

Functional postprocessing

Inter-run correlations

• Compute inter-run correlation for sub-170k compute_run_corr.py
• Make inter-run correlations maps with pycortex for sub-170k pycortex_maps_run_corr.py

PRF Gaussian fit

• Compute pRF gaussian grid fit derivatives for sub-170k compute_gauss_gridfit_derivatives.py
• Make pRF maps with pycortex for sub-170k pycortex_maps_gridfit.py

PRF ROIs

• Make ROIS files for sub-170k make_rois_img.py
• Create flatmaps of ROIs for sub-170k pycortex_maps_rois.py

PRF CSS fit

• Compute CSS statistics for sub-170k compute_css_stats.py
• Compute CSS fit derivatives for sub-170k compute_css_derivatives.py
• Compute CSS population cortical magnification (CM) for sub-170k compute_css_pcm.py
• Make CSS pRF fit derivatives and CM maps with pycortex for sub-170k pycortex_maps_css.py
• Make general TSV with CSS pRF fit derivatives, statistics and CM for sub-170k make_tsv_css.py
• Make ROIs figure of CSS pRF fit derivatives, statistics and CM for sub-170k and group make_rois_fig_tsv.py
• Make ROIs figure of CSS pRF fit derivatives, statistics and CM for sub-170k and group make_rois_fig.py
• Merge all figures for sub-170k and group merge_fig_css.py