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] [--version] [-v] [-q]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[-m MODEL] [-d DERIVATIVES [DERIVATIVES ...]]
[--derivative-label DERIVATIVE_LABEL] [--space SPACE]
[--force-index FORCE_INDEX [FORCE_INDEX ...]]
[--ignore IGNORE [IGNORE ...]] [--desc-label DESC_LABEL]
[--database-path DATABASE_PATH] [-s FWHM[:LEVEL:[TYPE]]]
[--n-cpus N_CPUS] [--mem-gb MEM_GB] [--debug] [--reports-only]
[-w WORK_DIR] [--drop-missing] [--estimator {nistats,afni}]
[--drift-model {polynomial,cosine,None}] [--error-ts]
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¶
- --version
show program’s version number and exit
- -v, --verbose
increase log verbosity for each occurrence, debug level is -vvv
- -q, --quiet
decrease log verbosity for each occurrence, debug level is -vvv
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
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
- --database-path
Path to directory containing SQLite database indices for this BIDS dataset. If a value is passed and the file already exists, indexing is skipped.
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 additive smoothing), isoblurto (isotropic smoothing progressivley applied till the target smoothness is reached). 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
- --mem-gb
maximum amount of memory to allocate across all processes
- --debug
run debug version of workflow
- --reports-only
skip running of workflow and generate reports
Other options¶
- -w, --work-dir
path where intermediate results should be stored
- --drop-missing
drop missing inputs/contrasts in model fitting.
- --estimator
Possible choices: nistats, afni
estimator to use to fit the model
- --drift-model
Possible choices: polynomial, cosine, None
specifies the desired drift model
- --error-ts
save error time series for first level models. Currently only implemented for afni estimator.