FitLins is a tool for estimating linear models, defined by the BIDS Model specification proposal, to BIDS-formatted datasets.
This software is in alpha stage, and should be considered unstable. Users are welcome to test the software, and open issues.
The CLI follows the BIDS-Apps convention:
Usage:
fitlins <bids_root> <out_dir> <analysis_level> [--model <model_name>]
See the output of fitlins --help
for all valid options:
usage: fitlins [-h] [-v]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-m MODEL] [-p PREPROC_DIR] [--space {MNI152NLin2009cAsym}]
[--debug]
bids_dir output_dir {run,session,participant,dataset}
FitLins: Workflows for Fitting Linear models to fMRI
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
{run,session,participant,dataset}
processing stage to be runa (see BIDS-Apps specification).
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Options for filtering BIDS queries:
--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
one or more participant identifiers (the sub- prefix can be removed)
-m MODEL, --model MODEL
location of BIDS model description (default bids_dir/model.json)
-p PREPROC_DIR, --preproc-dir PREPROC_DIR
location of preprocessed data (default output_dir/fmriprep)
--space {MNI152NLin2009cAsym}
registered space of input datasets
Options to handle performance:
--debug run debug version of workflow
At present, FitLins does not support smoothing or operate in subject-native space. It is developed against FMRIPREP-preprocessed datasets, but is intended to work with any dataset following the BIDS Derivatives draft specification.
FitLins is in Alpha-stage, and is not suitable for use as a library, as the internal organization may change substantially without deprecation periods. Similarly the outputs (or derivatives) are subject to change, as experience and user feedback prompt. The command-line interface outlined above should be fairly stable, however.