Usage

Execution and the BIDS format

The FitLins workflow takes as principal inputs a BIDS dataset, one or more derivative datasets, and a BIDS Stats Models file. We recommend using fMRIPrep for preprocessing your dataset.

The exact command to run fitlins depends on the Installation method. The common parts of the command follow the BIDS-Apps definition.

Example:

fitlins data/bids_root/ out/ participant \
    -d data/derivatives/fmriprep/ -w work/

Command-Line Arguments

FitLins: Workflows for Fitting Linear models to fMRI

usage: fitlins [-h] [-v]
               [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
               [-m MODEL] [-d DERIVATIVES [DERIVATIVES ...]]
               [--derivative-label DERIVATIVE_LABEL]
               [--space {MNI152NLin2009cAsym,}] [--force-index FORCE_INDEX]
               [--ignore IGNORE] [--desc-label DESC_LABEL]
               [-s FWHM[:LEVEL:[TYPE]]] [--n-cpus N_CPUS] [--debug]
               [-w WORK_DIR]
               bids_dir output_dir {run,session,participant,dataset}

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 output path for the outcomes of preprocessing and visual reports

analysis_level

Possible choices: run, session, participant, dataset

processing stage to be runa (see BIDS-Apps specification).

Named Arguments

-v, --version

show program’s version number and exit

Options for filtering BIDS queries

--participant-label

one or more participant identifiers (the sub- prefix can be removed)

-m, --model

location of BIDS model description

-d, --derivatives

location of derivatives (including preprocessed images).If none specified, indexes all derivatives under bids_dir/derivatives.

--derivative-label

execution label to append to derivative directory name

--space

Possible choices: MNI152NLin2009cAsym,

registered space of input datasets. Empty value for no explicit space.

--force-index

regex pattern or string to include files

--ignore

regex pattern or string to ignore files

--desc-label

use BOLD files with the provided description label

Options for preprocessing BOLD series

-s, --smoothing

Smooth BOLD series with FWHM mm kernel prior to fitting at LEVEL. Optional analysis LEVEL (default: l1) may be specified numerically (e.g., l1) or by name (run, subject, session or dataset). Optional smoothing TYPE (default: iso) must be one of: iso (isotropic). e.g., –smoothing 5:dataset:iso will perform a 5mm FWHM isotropic smoothing on subject-level maps, before evaluating the dataset level.

Options to handle performance

--n-cpus

maximum number of threads across all processes

--debug

run debug version of workflow

Other options

-w, --work-dir

path where intermediate results should be stored