Welcome to LIL Processing Docs

This documents the labs fmri-prep pipeline (as developed by Joe Heffernan). As documented here, this is the pipeline that is specific to the clinical epilepsy project. As such many of the scripts here are study specific.

Script Overview

This is a list of the relevant scripts. For a more detailed outline, see Overview

Pre-processing

  • run_tarred_dicom_info.py - creates a tsv file with dicom info
  • dicom_info.R - gets info from tsv file
  • run_heudiconv.py - convert dicoms to nifti
  • cli_adjust_jsons.py - check field maps
  • cli_post_heudiconv.py - update tsv file
  • run_fmriprep_epilepsy.py - run fmriprep on subject

GLM

  • generate_eprime_config.py - creates json file for each task
  • generate_events.py -
  • generate_design_matrix.py
  • run_deconvolve_prep.py
  • run_postproc_and_model_estimation.py

Post GLM

  • post_analysis.py
  • run_calculate_task_tsnr.py
  • deconvolve_link.py
  • PlotSingleParticipantMotion.R

General Notes

Within the language lab, there are 3 general pipelines used: 1. fmri-prep for clnical epilepsy data * The surfaces that are output here are freesurfer and hpc surfaces 2. HCP pipline for SOE data 3. AFNI-centric processing * Similar to using afni_proc.py, a lot of the SOE data is processed using afni-centric scripts