Usage notes
API
Command line API
bidspm is a SPM base BIDS app
Usage: bidspm [-h] [-v] --action
{preprocess,smooth,default_model,create_roi,stats,contrasts,results}
[--verbosity {0,1,2}] [--task TASK [TASK ...]]
[--space SPACE [SPACE ...]]
[--ignore {fieldmaps,slicetiming,unwarp,qa,contrasts,transformations,dataset} [{fieldmaps,slicetiming,unwarp,qa,contrasts,transformations,dataset} ...]]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--boilerplate_only] [--dry_run]
[--bids_filter_file BIDS_FILTER_FILE] [--fwhm FWHM]
[--options OPTIONS] [--skip_validation] [--roi_dir ROI_DIR]
[--roi_name ROI_NAME [ROI_NAME ...]] [--anat_only]
[--dummy_scans DUMMY_SCANS]
[--roi_atlas {neuromorphometrics,wang,anatomy_toobox,visfatlas,hcpex}]
[--model_file MODEL_FILE] [--preproc_dir PREPROC_DIR]
[--keep_residuals] [--concatenate] [--design_only] [--roi_based]
bids_dir output_dir {subject,dataset}
Positional Arguments
- bids_dir
Fullpath to the directory with the input dataset formatted according to the BIDS standard.
- output_dir
Fullpath to the directory where the output files will be stored.
- analysis_level
Possible choices: subject, dataset
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
- -v, --version
show program’s version number and exit
- --action
Possible choices: preprocess, smooth, default_model, create_roi, stats, contrasts, results
Action to perform.
- --verbosity
Possible choices: 0, 1, 2
Verbosity level.
Default: 2
- --task
Tasks of the input data.
- --space
Space of the input data.
Default: [‘IXI549Space’]
- --ignore
Possible choices: fieldmaps, slicetiming, unwarp, qa, contrasts, transformations, dataset
To specify steps to skip.
- --participant_label
The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include “sub-“). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list. Can be a regular expression. Example:
'01', '03', '08'
.- --boilerplate_only
When set to
true
this will only generate figures describing the raw data, the methods section boilerplate.Default: False
- --dry_run
When set to
true
this will generate and save the SPM batches, but not actually run them.Default: False
- --bids_filter_file
Fullpath to a JSON file describing custom BIDS input filters.
- --fwhm
The full width at half maximum of the gaussian kernel to apply to the preprocessed data or to use as inputs for the statistical analysis.
Default: 6.0
- --options
Path to JSON file containing bidspm options.
- --skip_validation
To skip BIDS dataset and BIDS stats model validation.
Default: False
- --roi_dir
Fullpath to the directory with the regions of interest.
- --roi_name
Name of the roi to create. If the ROI does not exist in the atlas, the list of available ROI will be returned in the error message.
preprocess only arguments
- --anat_only
If preprocessing should be done only on anatomical data.
Default: False
- --dummy_scans
Number of dummy scans to remove.
Default: 0
create roi only arguments
- --roi_atlas
Possible choices: neuromorphometrics, wang, anatomy_toobox, visfatlas, hcpex
Atlas to create the regions of interest from.
Default: “neuromorphometrics”
stats only arguments
- --model_file
Fullpath to BIDS stats model.
- --preproc_dir
Fullpath to the directory with the preprocessed data.
- --keep_residuals
Keep GLM residuals.
Default: False
- --concatenate
To create 4D image of all the beta and contrast images of the conditions of interest included in the run level design matrix.
Default: False
- --design_only
To only specify the GLM without estimating it.
Default: False
- --roi_based
To run stats only in regions of interests.
Default: False
all parameters use
snake_case
,most “invalid” calls simply initialize bidspm.
For a more readable version of this help section, see the online https://bidspm.readthedocs.io/en/latest/usage_notes.html.