scripts

The structure of the scripts and their usage:

• setup:
  • bash setup_venv.sh: Sets up the Python enviornment and installs some dependencies
  • condor_submit build_*.submit: Build Singularity container image of FreeSurfer, fMRIPrep and Micapipe
• proc_anat: Processes T1w images using FreeSurfer
  • bash get_submit.sh <dataset> [<n>]: Generates condor job instructions to run FreeSurfer on <n> (default: all the remaining) subjects of <dataset>. The jobs can be run by feeding the printed instruction to condor_submit via bash get_submit.sh <dataset> [<n>] | condor_submit.
  • bash run_freesurfer.sh <dataset> <subject_id>: Runs FreeSurfer (through Singularity) on a given subject
• proc_rest: Processes the rs-fMRI data and creates functional connectivity and functional connectivity dynamics matrices
  • bash gen_submit.sh <dataset> [<n> <cpus=1> <skip_excluded=true>]: Generates condor job instructions to run proc_rest.sh on <n> (default: all the remaining) subjects of <dataset>. The jobs can be run by feeding the printed instruction to condor_submit via bash get_submit.sh <dataset> [<n> <cpus=1> <skip_excluded=true>] | condor_submit.
  • bash proc_rest.sh <dataset> <subject_id> [<cpus=1>]: Runs fMRIPrep (through singularity) and post-processing of its output (post_fmriprep.py) on a given subject.
  • python post_fmriprep.py <dataset> <subject_id> [<session>]: Runs post-processing of fMRIprep output including parcellation, cleaning and calculation of FC and FCD. It is run as part of proc_rest.sh.
• proc_dwi: Processes the dwi data (and anatomical data, as required by Micapipe) and creates structural connectivity strength and length matrices.
  • bash gen_submit.sh <dataset> [<n> <cpus=1> <skip_excluded=true>]: Generates condor job instructions to run proc_dwi.sh on <n> (default: all the remaining) subjects of <dataset>. The jobs can be run by feeding the printed instruction to condor_submit via bash get_submit.sh <dataset> [<n> <cpus=1> <skip_excluded=true>] | condor_submit.
  • bash proc_dwi.sh <dataset> <subject_id>: Runs DWI and T1w processing of Micapipe (through singularity) as well as post-processing of its output (post_micapipe.py) on a given subject.
  • python post_micapipe.py <dataset> <subject_session_id>: Runs post-processing of micapipe output which includes labeling and normalization of the SC matrices.
• group: Group-pooling of the structural and functional connectivity data.
  • python group_fc.py <dataset> <fc_file_prefix> [<group_name> <sub1> <sub2> ...]: Pools specified FC and FCD data of a group of subjects. If no group_name and list of subjects are provided will group all the available subjects.
  • python group_sc.py <dataset> [<group_name> <sub1> <sub2> ...]: Pools SC strength and length data of a group of subjects. If no group_name and list of subjects are provided will group all the available subjects.
• modeling: Biophysical network modeling.
  • run/: Runs BNM simulation-optimizations and other simulation experiments. See ./modeling/run/ for details.
  • check_fit.py: Loads the bnm_cuda CMAES and simulation outputs and processes them for the statistical analyses.
• utils: A module that can be imported by other scripts and includes utility functions for:
  • datasets.py: Load data (e.g. the six maps).
  • plot.py: Plotting functions.
  • stats.py: Statistical functions.
  • transform.py: Parcellation and deparcellation.
• src: Includes the parcellation, templates and PET images of NMDA and GABA_A. Source of each file is described in ./src/.