Standalone command line usage

SDCFlows can execute fieldmap estimation from a BIDS-compliant dataset by using the standalone command line interface:

SDCFlows 0+unknown

Estimate fieldmaps available in a BIDS-compliant MRI dataset.

usage: sdcflows [-h] [--version] [-v]
                [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--session-label [SESSION_LABEL ...]]
                [--bids-filter-file PATH] [--bids-database-dir PATH]
                [--bids-database-wipe] [--nprocs NPROCS]
                [--omp-nthreads OMP_NTHREADS] [--mem-gb MEMORY_GB] [--debug]
                [--pdb] [--sloppy] [-w WORK_DIR] [-n] [--no-fmapless]
                [--use-plugin USE_PLUGIN] [--notrack]
                bids_dir output_dir
                {participant,group} [{participant,group} ...]

Positional Arguments

bids_dir

The root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).

output_dir

The directory where the output files should be stored. If you are running group level analysis this folder should be prepopulated with the results of the participant level analysis.

analysis_level

Possible choices: participant, group

Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel) using the same output_dir.

Named Arguments

--version

show program’s version number and exit

-v, --verbose

Increases log verbosity for each occurrence, debug level is -vvv.

Default: 0

Options related to BIDS

--participant-label

A space delimited list of participant identifiers or a single identifier (the sub- prefix can be removed).

--session-label

Filter input dataset by session label.

--bids-filter-file

a JSON file describing custom BIDS input filter using pybids {<suffix>:{<entity>:<filter>,…},…} (https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)

--bids-database-dir

Path to an existing PyBIDS database folder, for faster indexing (especially useful for large datasets).

--bids-database-wipe

Wipe out previously existing BIDS indexing caches, forcing re-indexing.

Default: False

Options to handle performance

--nprocs

Maximum number of simultaneously running parallel processes executed by SDCFlows (e.g., several instances of ANTs’ registration). However, when --nprocs is greater or equal to the --omp-nthreads option, it also sets the maximum number of threads that simultaneously running processes may aggregate (meaning, with --nprocs 16 --omp-nthreads 8 a maximum of two 8-CPU-threaded processes will be running at a given time). Under this mode of operation, --nprocs sets the maximum number of processors that can be assigned work within an SDCFlows job, which includes all the processors used by currently running single- and multi-threaded processes. If None, the number of CPUs available will be automatically assigned (which may not be what you want in, e.g., shared systems like a HPC cluster.

--omp-nthreads

Maximum number of threads that multi-threaded processes executed by SDCFlows (e.g., ANTs’ registration) can use. If None, the number of CPUs available will be automatically assigned (which may not be what you want in, e.g., shared systems like a HPC cluster.

--mem-gb

Upper bound memory limit for SDCFlows processes.

--debug

Enable changes to processing to aid in debugging

Default: False

--pdb

Open Python debugger (pdb) on exceptions.

Default: False

--sloppy

Use sloppy mode for minimal footprint.

Default: False

Instrumental options

-w, --work-dir

Path where intermediate results should be stored.

Default: /home/runner/work/sdcflows/sdcflows/docs/work

-n, --dry-run

only find estimable fieldmaps (that is, estimation is not triggered)

Default: False

--no-fmapless

Allow fieldmap-less estimation

Default: True

--use-plugin

Nipype plugin configuration file.

--notrack

Opt-out of sending tracking information of this run to the NiPreps developers. This information helps to improve SDCFlows and provides an indicator of real world usage for obtaining funding.

Default: False