FitLins - Fitting Linear Models to BIDS Datasets

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.

Warning

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.