abcd-bids-tfmri-pipeline

Purpose

This tool can be used to complete Level 1 and Level 2 analyses of task fMRI dtseries data. Specifically, this tool was designed to work with data that were minimally processed using the DCAN Labs' ABCD-HCP-Pipeline, including their Collection 3165 release through NDA. Inputs must be in the same format as ABCD-HCP-Pipeline outputs after running filemap. The files output from this pipeline were fully processed and prepared for higher-level statistics.

Requirements and Dependencies

Python 3.6.13 or greater
Washington University Workbench Command (wb_command)
FMRIB Software Library (FSL) v6.0.4
Python numpy package
Python pandas package

Usage

Installation

Clone this repository into a new directory on your local filesystem.
Install the required Python modules using pip.
To verify that the code is set up, run python3 pipeline_wrapper.py --help within that same directory.

Once this repository is cloned into a local directory, and all of its dependencies are also downloaded onto the local filesystem, no further installation or setup is required. Running this pipeline on multiple subjects at once will require a SLURM cluster.

Required Arguments

--subject takes one string, the ID of the subject to process. If it does not start with the prefix sub-, that prefix will be added.
--ses takes one string, the name of the session that you are running the pipeline on. If it does not start with the prefix ses-, that prefix will be added.
--task takes one string, the name of the task that you are running the pipeline on.
--study-dir takes a valid path to the existing BIDS base study directory. The --study-dir should have a subdirectory called derivatives, which should have a subdirectory called abcd-hcp-pipeline (or called something else, which the user can provide with the --bids-dir argument).
--events-dir takes a valid path to a real directory containing event .tsv files. --events-dir is required unless running a certain kind of level 1 analysis. This flag is necessary unless the level 1 .fsf file specifies that the basic waveform shape of each EV model is square. Include this flag unless the level 1 .fsf file contains the line set fmri(shape1) 0.
--output takes a valid directory path to save pipeline outputs into. If the provided --output directory does not already exist, then this script will create a new directory at that path.
--wrapper-location takes a valid path to this directory containing pipeline_wrapper.py.
- Currently, an error may occur if this argument is excluded. In future versions of the pipeline, including this argument will not be necessary unless running the pipeline (or its sub-scripts) in parallel using SLURM.

Example Call

To run this pipeline on one subject from the Linux/Unix command-line terminal, use a command that looks like this:

fsl_dir=/home/software/fsl/bin/
subject_ID=sub-ABCDEFGH
session_ID=ses-QRSTUV
task_name=my_task
study_dir=/home/users/shared/data/my_study
wb_command=/home/software/workbench/bin/wb_command
events_dir=/home/users/shared/data/task_events/
wrapper_dir=.

python3 pipeline_wrapper.py --subject ${subject_ID} --ses ${session_ID} --study-dir ${study_dir} --task ${task_name} --events-dir ${events_dir} --fsl-dir ${fsl_dir} --wb-command ${wb_command} --wrapper-location ${wrapper_dir}

Other Arguments/Options

Arguments With Default Values

Often, the following arguments are unnecessary because they have default values that the pipeline will use. But the user can change them by including these arguments explicitly.

Files for GLMs

--template1 accepts a string, the base name (but not the full path) of the Level 1 .fsf template file. By default, the pipeline will assume that the --template1 filename is template_DCAN_version_(--task)_level1_UPDATED_FINAL.fsf.
--template2 accepts a string, the base name (but not the full path) of the Level 2 .fsf template file. By default, the pipeline will assume that the --template2 filename is template_DCAN_version_(--task)_level2_UPDATED_FINAL.fsf.

Information for GLMs

Runs

--runs takes 1 or more positive integers, each subject's number of runs. The integers must be provided as a space-delimited list, such as 1 2 3 4 for runs 1 through 4. By default, this argument's value(s) will be 1 2.
--levels takes up to 2 positive integers, the levels to conduct the analysis on: 1 for one run, and/or 2 to merge multiple runs. By default, both levels will be run.

Censoring

--censor takes a positive integer, the number of initial frames/volumes to censor. By default, this argument's value will be 2.
--fd takes one decimal number between 0 and 1, the framewise displacement threshold for censoring volumes with high motion. By default, this argument's value will be 0.9.

Smoothing

--spat-smooth takes one positive integer, the number of millimeters of spatial smoothing that you want for the surface and volume data. By default, this argument's value will be 0.
--surf-smooth takes one positive integer, the number of millimeters of surface smoothing that has already been applied in the minimal processing steps. By default, this argument's value will be 0.
--vol-smooth takes one positive integer, the number of millimeters of volume smoothing that has already been applied in the minimal processing steps. By default, this argument's value will be 0.

Highpass Filtering

--filter takes one positive integer, the high pass temporal filter cutoff (in seconds). By default, this argument's value will be 100.

Paths

--bids-dir takes one string, the name of the BIDS-standard file-mapped directory with subject data in the "derivatives" subdirectory of your --study-dir. This argument is only needed if your BIDS directory is called something other than abcd-hcp-pipeline.
- This path should be valid: (--study-dir)/derivatives/(--bids-dir)/(--subject)/(--ses)/func/sub-(--subject)_ses-(--ses)_task-(--task)_run-(--runs)_bold_timeseries.dtseries.nii
--temp-dir takes a valid path to a directory to save temporary files into. By default, the pipeline will look for a folder called temp in the level-1 subdirectory of the --output folder. If no folder exists at the --temp-dir path, then the pipeline will create an empty folder there.
--templates takes a valid path to an existing directory which contains all of the required template .fsf files. By default, the pipeline will use a folder called templates/ in the same file location as the main pipeline script (pipeline_wrapper.py), the top level of this repository.

Naming Conventions

--study-name takes one string, the name of the study that you are running the pipeline on. If no --study-name is given by the user, then the pipeline will give the outputs the default study name of ABCD.

Optional Arguments for Different Run Modes

Each of these flags is unnecessary, but if included, will change the mode in which the pipeline runs.

--help takes no parameters. Include this flag to show this help message and exit.
--keep-all takes no parameters. Include this flag to keep all files generated during the pipeline. By default, the pipeline will only keep .dtseries.nii, dof, log, and event files.
--overwrite takes no parameters. Include this flag to overwrite files at the --output directory. By default, the script will end if files exist there.
--no-parallel takes no parameters. By default, the pipeline script will use Python's multiprocessing module to process level 1 analysis runs in parallel simultaneously. Include this flag for the script to process the analyses sequentially instead. Using this flag is not recommended when the user can run the pipeline on multiple cores, because running the analyses sequentially will significantly increase the pipeline's operating time.

Quasi-Required Arguments

These arguments are usually required, except in special circumstances.

These arguments are paths to software libraries required to run the task pipeline. By default, the pipeline will try to infer the paths. But if that fails, then the user needs to give them explicitly. So, --fsl-dir and --wb-command are required unless the user has certain paths already saved as BASH environment variables.

--fsl-dir takes a valid path to the existing FreeSurfer bin directory containing the executable files fsl, fslmerge, fslmaths, flameo, and feat_model from the FMRIB Software Library (FSL). If this flag is excluded, then the script will try to guess the path to the FSL by checking the user's BASH aliases.
--wb-command takes a valid path to the existing wb_command executable file to run Workbench Command. If this flag is excluded, then the script will try to guess the path to the wb_command file by checking the user's BASH aliases.

SLURM/SBATCH Arguments for run_sbatch_jobs.py

pipeline_wrapper.py is the main script to run the pipeline on one task of one session of one subject. Use run_sbatch_jobs.py to run multiple subjects/sessions/tasks at once using a SLURM cluster. The arguments below are not needed to run 1 subject using pipeline_wrapper.py but are needed to run multiple subjects in parallel using run_sbatch_jobs.py

--account takes one string, the name of the account to submit each SBATCH job under.
--cpus takes one integer, the number of CPUs to use for each SBATCH/SLURM job. By default, this argument's value will be 1.
--memory takes one integer, the memory in gigabytes (GB) to assign to each sbatch job. The default number is 8.
--print-progress takes no parameters. Include this flag for the script to print updates about its progress at intervals defined by --sleep. This will also print every command that is run to submit a pipeline batch job.
--sleep takes one integer, the number of seconds to wait between batch job submissions. The default number is 10.
--time takes a string formatted specifically as HH:MM:SS where HH is hours, MM is minutes, and SS is seconds. This argument is the time limit for each ABCD-BIDS-task-fmri-pipeline SBATCH/SLURM job. 01:00:00 is the default time limit.

Current Issues

The current version of the pipeline might crash if the user is not aware of how to avoid certain pitfalls. Future versions of the pipeline will aim to fix all of these issues.

An error may occur unless...

The --output directory matches the location of the .fsf template file FEAT directory containing the subdirectories level-1 and level-2.
The --events-dir location matches the level-1 subdirectory of the .fsf template file FEAT directory.
The --template[x] flags are filenames only, and not full file paths.
The --wrapper-location argument is explicitly included.
- Although the script is supposed to infer its own location (except when run using SBATCH), there may still be cases where the script needs its location explicitly passed in.
Only one task per subject session is run at a time, or --keep-all is explicitly included.
- Without the --keep-all flag, running the pipeline on one task may overwrite/delete the outputs of a simultaneous pipeline run on another task.

Future Features

Future versions of the pipeline will hopefully

be able to run multiple tasks in one script call
not need --wrapper-location unless running run_sbatch_jobs.py

Outputs

The pipeline will produce its outputs in the following BIDS-valid directory structure:

output_dir
├── level-1
│   ├── events
│   │   └── sub-*_ses-*_task-*_run-*.tsv
│   ├── level1_run-*
│   │   ├── sub-*_ses-*_task-*_run-*_cope*.dtseries.nii
│   │   ├── sub-*_ses-*_task-*_run-*_dof
│   │   ├── sub-*_ses-*_task-*_run-*_logfile
│   │   └── sub-*_ses-*_task-*_run-*_res4d.dtseries.nii
│   └── temp
└── level-2
    ├── cope_files
    │   └── sub-*_ses-*_task-*_contrast_*_cope*.dtseries.nii
    ├── dof_files
    │   └── sub-*_ses-*_task-*_contrast_*_tdof_t1.dtseries.nii
    ├── log_files
    │   └── sub-*_ses-*_task-*_contrast_*_logfile
    ├── mask_files
    │   └── sub-*_ses-*_task-*_contrast_*_mask.dtseries.nii
    └── res4d_files
        └── sub-*_ses-*_task-*_contrast_*_res4d.dtseries.nii

Metadata

Information about this README file:

Created on 2020-10-22 by Eric Feczko (@EricFeczko)
Updated on 2021-12-03 by Greg Conan (@GregConan)

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