├── .gitignore ├── README.md ├── analysis └── README.md ├── auxil ├── README.md ├── archive │ ├── README.txt │ └── subid_list.txt ├── fsl_designs │ └── templates │ │ └── restROI_design.fsf ├── onsets │ └── README.txt ├── ref │ └── icbm152_gm25_spm12mask.nii ├── roi_masks │ └── yeo2011 │ │ └── gen_utils │ │ └── FSL_17Networks_lib.nii.gz ├── runorders │ └── .empty.txt └── study_info.par ├── output └── README.md ├── prep └── README.md ├── qa └── README.md ├── raw └── README.md └── scripts ├── BXH_QA ├── bxh_generate ├── overview_generate ├── run_BXH_qa └── sfnr.py ├── README.md ├── globals.m ├── globals.par ├── group_level ├── glm │ ├── run_rfx_SPM12W │ ├── run_tfce_FSL │ ├── sbatch_rfx_SPM12W │ └── tfce.par └── roi │ ├── par_roi.m │ └── run_roi_SPM12W ├── import_data ├── get_conversion_names.py ├── par_import.json ├── run_import_from_labvol ├── sbatch_bids_to_damn └── sbatch_dcm_to_bids ├── init_project ├── preprocess ├── matlab_prep_DARTEL.m ├── matlab_prep_SPM12W.m ├── pfile_template_DARTEL.txt ├── pfile_template_FSL.txt ├── pfile_template_SPM12W.txt ├── prep.par ├── run_prep ├── sbatch_prep_DARTEL ├── sbatch_prep_FSL ├── sbatch_prep_SPM12W └── sbatch_prep_TOPUP ├── retrieve_dcm ├── retrieve_from_conquest ├── sub_level ├── glm │ ├── matlab_glm_SPM12W.m │ ├── matlab_glm_masking.m │ ├── par_glm.m │ ├── run_glm_SPM12W │ └── sbatch_glm_SPM12W └── roi │ ├── gen_ventricle_mask │ ├── generate_roimasks │ ├── generate_yeo_roimasks │ ├── rest.par │ ├── run_rest_FSL │ ├── sbatch_rest_glm_FSL │ ├── sbatch_rest_preglm_FSL │ └── sbatch_rest_timecourse_FSL └── utils ├── clean_up_prep ├── cleanup_output ├── copy_dartel_output ├── finish_log ├── funcs ├── p_globals_template.txt ├── run_convert ├── sbatch_convert ├── setup_backup_dirs ├── write_p_globals └── write_pfile /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PrincetonUniversity/prsonpipe/HEAD/.gitignore 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