Usage notes#

API#

bidspmHelp()#

General intro function for bidspm

Note

  • all parameters use snake_case

  • most “invalid” calls simply initialize bidspm

BIDS APP CALLS

generic call:

bidspm(bids_dir, output_dir, analysis_level, ...
       'action', 'some_action', ...
       'participant_label', {}, ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'verbosity', 2, ...
       'options', struct([]))

Obligatory parameters

Parameters:

  • bids_dir (path) – path to a raw BIDS dataset

  • output_dir (path) – path where to output data

  • analysis_level (string) – Can either be 'subject' or 'dataset'. Defaults to 'subject'

  • action (char) –

    defines the pipeline to run; can be any of:

    • 'copy': copies fmriprep data for smoothing

    • 'preprocess': preprocesses data

    • 'smooth': smooths data

    • 'default_model': creates a default BIDS stats model

    • 'create_roi': creates ROIs from a given atlas

    • 'stats': runs model specification / estimation, contrast computation, display results

    • 'contrasts': runs contrast computation, display results

    • 'results': displays results

    • 'bms': performs bayesian model selection

    • 'specify_only' only specifies the models

  • participant_label (cellstr) – cell of participants labels. For example: {'01', '03', '08'}. Can be a regular expression. Defaults to {}

  • bids_filter_file (path) – path to JSON file or structure

  • verbosity (positive integer) – can be any value between 0 and 3. Defaults to 2

  • options (path to JSON file or structure) – See the checkOptions help to see the available options.

Note

Arguments passed to bidspm have priorities over the options defined in opt. For example passing the argument 'dry_run', true will override the option opt.dryRun =  false.

PREPROCESSING

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'preprocess', ...
       'participant_label', {}, ...
       'task', '', ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'verbosity', 2, ...
       'options', struct([]), ...
       'boilerplate_only', false, ...
       'dry_run', false, ...
       'dummy_scans', 0, ...
       'anat_only', false, ...
       'ignore', {}, ...
       'fwhm', 6, ...
       'skip_validation', false)
Parameters:

  • boilerplate_only (logical) – Only creates dataset description reports. and methods description. Defaults to false.

  • space (cell string) – Defaults to {}

  • task (char) – Only a single task can be processed at once. Defaults to ''.

  • dry_run (logical) – Defaults to false

  • dummy_scans (positive scalar) – Number of dummy scans to remove. Defaults to 0.

  • anat_only (logical) – Only preprocesses anatomical data. Defaults to false.

  • ignore (cellstr) – can be any of {'fieldmaps', 'slicetiming', 'unwarp', 'qa'}

  • fwhm (positive scalar) – Smoothing to apply to the preprocessed data. Defaults to 6.

  • skip_validation (logical) – To skip bids dataset or bids stats model validation. Defaults to false.

COPY

Copies and unzips input data to output dir. For example for fmriprep data before smoothing.

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'copy', ...
       'participant_label', {}, ...
       'task', {}, ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'verbosity', 2, ...
       'options', struct([]), ...
       'anat_only', false, ...
       'force', false)
Parameters:

  • space (cell string) – Defaults to {}

  • task (char or cell string) – Defaults to {}

  • force (logical) – Overwrites previous data if true. Defaults to false.

  • anat_only (logical) – Only copies anatomical data. Defaults to false.

CREATE_ROI

Creates ROIs from a given atlas.

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'create_roi', ...
       'participant_label', {}, ...
       'space', {'MNI'}, ...
       'bids_filter_file', struct([]), ...
       'preproc_dir', preproc_dir, ...
       'verbosity', 2, ...
       'options', struct([]), ...
       'roi_atlas', 'wang', ...
       'roi_name', {'V1v', 'V1d'}, ...
       'hemisphere', {'L', 'R'})
Parameters:

  • space (cell string) – Defaults to {}

  • roi_atlas (char) –

    Can be any of:

    • 'visfatlas'

    • 'anatomy_toobox'

    • 'neuromorphometrics'

    • 'hcpex'

    • 'wang'

    • 'glasser'

    Defaults to 'neuromorphometrics'

  • roi_name (cell string) – 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.

  • hemisphere (cell string containing any of 'L', 'R') – Hemisphere of the ROI to create. Not all ROIs have both hemispheres. Defaults to {'L', 'R'}.

  • preproc_dir (path) – path to preprocessed data Necessary when using 'T1w' or 'individual' space to access deformation fields to inverse normalize ROIs.

SMOOTH:

Copies files to output dir and smooths them.

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'smooth', ...
       'participant_label', {}, ...
       'task', {}, ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'options', struct([]), ...
       'verbosity', 2, ...
       'fwhm', 6, ...
       'dry_run', false)
Parameters:

  • space (cell string) – Defaults to {}

  • task (char or cell string) – Defaults to {}

  • fwhm (positive scalar) – Smoothing to apply to the preprocessed data. Defaults to 6.

  • dry_run (logical) – Defaults to false.

  • anat_only (logical) – Only smooths the anatomical data. Defaults to false.

CREATE DEFAULT_MODEL

Creates a default BIDS stats model for a given raw BIDS dataset.

bidspm(bids_dir, output_dir, 'dataset', ...
       'action', 'default_model', ...
       'participant_label', {}, ...
       'task', {}, ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'verbosity', 2, ...
       'options', struct([]), ...
       'options', struct([]), ...
       'ignore', {}, ...
       'skip_validation', false)
Parameters:

  • space (cell string) – Defaults to {}

  • task (char or cell string) – Defaults to {}

  • ignore (cell string) – can be any of {'contrasts', 'transformations', 'dataset'}

  • skip_validation (logical) – To skip bids dataset or bids stats model validation. Defaults to false.

STATS

Note

  • 'stats' runs model specification / estimation, contrast computation, display results

  • 'contrasts' runs contrast computation, display results

  • 'results' displays results

  • 'specify_only' only specifies the models

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'stats', ...
       'participant_label', {}, ...
       'task', {}, ...
       'space', {'individual', 'IXI549Space'}, ...
       'bids_filter_file', struct([]), ...
       'options', struct([]), ...,
       'verbosity', 2, ...
       'preproc_dir', preproc_dir, ...
       'model_file', model_file, ...          % specific to stats
       'fwhm', 6, ...
       'dry_run', false, ...
       'boilerplate_only', false, ...
       'roi_atlas', 'neuromorphometrics', ...
       'roi_based', false, ...
       'roi_dir', '', ...
       'roi_name', {''}, ...
       'design_only', false, ...
       'ignore', {}, ...
       'concatenate', false, ...
       'use_dummy_regressor', false)
       'skip_validation', false)

Obligatory parameters

Parameters:

  • preproc_dir (path) – path to preprocessed data

  • model_file (path to JSON file or dir or structure) – Path to the BIDS model file that contains the model to specify and the contrasts to compute. A path to a dir can be passed as well. In this case all *_smdl.json files will be used and looped over. This can useful to specify several models at once Before running Bayesion model selection on them.

  • space (cell string) – Defaults to {}

Optional parameters

Parameters:

  • fwhm (positive scalar) – smoothing level of the preprocessed data

  • design_only (logical) – to only run the model specification

  • ignore (cell string) – can be any of {'qa'}, to skip quality controls into a single 4D image.

  • concatenate (logical) – will concatenate the beta images of the conditions of interest convolved by an HRF.

  • dry_run (logical) – Defaults to false.

  • roi_atlas (char) – Name of the atlas to use to label activations in MNI space.

  • roi_based (logical) – Set to true to run a ROI-based analysis. Defaults to false.

  • roi_dir (path) – Path to the directory containing the ROIs.

  • roi_name (cell string) – Names or regex expression of the ROI to use.

  • boilerplate_only (logical) – Only creates dataset description reports. and methods description. Defaults to false.

  • use_dummy_regressor (logical) – If true any missing condition will be modelled by a dummy regressor of NaN. Defaults to false.

  • skip_validation (logical) – To skip bids dataset or bids stats model validation. Defaults to false.

  • node_name (char) – Model node to run.

BAYESIAN MODE SELECTION

bidspm(bids_dir, output_dir, 'subject', ...
       'action', 'bms', ...
       'participant_label', {}, ...
       'options', struct([]), ...,
       'verbosity', 2, ...
       'models_dir', models_dir, ...
       'fwhm', 6, ...
       'dry_run', false, ...
       'skip_validation', false)
Parameters:

  • action (char) – Any of: {'bms', 'bms-posterior', 'bms-bms'} ‘bms’ will performm all steps for the baeysian model selection. If ‘bms’ has been performed then 'bms-posterior' can``’bms-bms’`` be performed one after the other. See the help section of bidsModelSelection() for more details.

  • models_dir – A path to a dir can be passed as well. In this case all *_smdl.json files will be used and looped over.

  • dry_run (logical) – Defaults to false.

  • fwhm (positive scalar) – smoothing level of the preprocessed data

  • skip_validation (logical) – To skip bids dataset or bids stats model validation. Defaults to false.

Note

For the bayesian model selection to function you must first specify all your models using the 'specify_only' action with the options 'use_dummy_regressor', true.

opt.glm.useDummyRegressor = true;

bidspm(bids_dir, output_dir, 'subject', ...
      'participant_label', participant_label, ...
      'preproc_dir', preproc_dir, ...
      'action', 'specify_only', ...
      'model_file', models_dir, ...
      'use_dummy_regressor', true
      'fwhm', FWHM);

low level calls

USAGE:

% initialise (add relevant folders to path)
bidspm

% equivalent to
bidspm init
bidspm('action', 'init')

% help
bidspm help
bidspm('action', 'help')

% uninitialise (remove relevant folders from path)
bidspm uninit
bidspm('action', 'uninit')

% also adds folder for testing to the path
bidspm dev
bidspm('action', 'dev')

% tried to update the current branch from the upstream repository
bidspm update
bidspm('action', 'update')

% misc
bidspm version
bidspm('action', 'version')

bidspm run_tests
bidspm('action', 'run_tests')

For a more readable version of this help section, see the online <a href=”https://bidspm.readthedocs.io/en/latest/usage_notes.html”>documentation</a>.

Command line API#

bidspm is a SPM base BIDS app

Usage: bidspm [-h] [-v]
              bids_dir output_dir {subject,dataset}
              {preprocess,smooth,default_model,create_roi,stats,contrasts,results,bms}
              ...

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 wsub_command_parserill be performed. Multiple participant level analyses can be run independently (in parallel) using the same output_dir.

command

Possible choices: preprocess, smooth, default_model, create_roi, stats, contrasts, results, bms

Choose a subcommand

Named Arguments#

-v, --version

show program’s version number and exit

Sub-commands#

preprocess#

Preprocessing

bidspm preprocess [-h]
                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                  [--verbosity {0,1,2,3}]
                  [--bids_filter_file BIDS_FILTER_FILE] [--options OPTIONS]
                  [--boilerplate_only] [--anat_only]
                  [--dummy_scans DUMMY_SCANS] [--task TASK [TASK ...]]
                  [--space SPACE [SPACE ...]] [--fwhm FWHM] [--dry_run]
                  [--skip_validation]
                  [--ignore {fieldmaps,slicetiming,unwarp,qa} [{fieldmaps,slicetiming,unwarp,qa} ...]]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--boilerplate_only

When set to true this will only generate figures describing the raw data, the methods section boilerplate.

Default: False

--anat_only

If preprocessing should be done only on anatomical data.

Default: False

--dummy_scans

Number of dummy scans to remove.

Default: 0

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--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

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

--ignore

Possible choices: fieldmaps, slicetiming, unwarp, qa

To specify steps to skip.

smooth#

Smooth

bidspm smooth [-h]
              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
              [--verbosity {0,1,2,3}] [--bids_filter_file BIDS_FILTER_FILE]
              [--options OPTIONS] [--task TASK [TASK ...]]
              [--space SPACE [SPACE ...]] [--fwhm FWHM] [--anat_only]
              [--dry_run]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--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

--anat_only

If preprocessing should be done only on anatomical data.

Default: False

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

default_model#

Create default model

bidspm default_model [-h]
                     [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                     [--verbosity {0,1,2,3}]
                     [--bids_filter_file BIDS_FILTER_FILE] [--options OPTIONS]
                     [--task TASK [TASK ...]] [--space SPACE [SPACE ...]]
                     [--skip_validation]
                     [--ignore {Transformations,Contrasts,Dataset} [{Transformations,Contrasts,Dataset} ...]]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

--ignore

Possible choices: Transformations, Contrasts, Dataset

To specify steps to skip.

create_roi#

Create ROIs

bidspm create_roi [-h]
                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                  [--verbosity {0,1,2,3}]
                  [--bids_filter_file BIDS_FILTER_FILE] [--options OPTIONS]
                  [--boilerplate_only] [--space SPACE [SPACE ...]] --roi_name
                  ROI_NAME [ROI_NAME ...]
                  [--roi_atlas {glasser,wang,neuromorphometrics,hcpex,anatomy_toobox,visfatlas}]
                  [--preproc_dir PREPROC_DIR] [--hemisphere {L,R} [{L,R} ...]]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--boilerplate_only

When set to true this will only generate figures describing the raw data, the methods section boilerplate.

Default: False

--space

Space of the input data.

Default: ['IXI549Space']

--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.

--roi_atlas

Possible choices: glasser, wang, neuromorphometrics, hcpex, anatomy_toobox, visfatlas

Atlas to create the regions of interest from.

Default: 'neuromorphometrics'

--preproc_dir

Fullpath to the directory with the preprocessed data.

--hemisphere

Possible choices: L, R

To specify steps to skip.

stats#

Specify and estimate GLM, compute contrasts and get results

bidspm stats [-h]
             [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
             [--verbosity {0,1,2,3}] [--bids_filter_file BIDS_FILTER_FILE]
             [--options OPTIONS] --model_file MODEL_FILE
             [--preproc_dir PREPROC_DIR] [--task TASK [TASK ...]]
             [--space SPACE [SPACE ...]] [--fwhm FWHM] [--dry_run]
             [--skip_validation] [--boilerplate_only] [--keep_residuals]
             [--design_only] [--use_dummy_regressor]
             [--ignore {qa} [{qa} ...]] [--roi_based] [--roi_dir ROI_DIR]
             [--roi_name ROI_NAME [ROI_NAME ...]] [--node_name NODE_NAME]
             [--concatenate]
             [--roi_atlas {glasser,wang,neuromorphometrics,hcpex,anatomy_toobox,visfatlas}]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--model_file

Fullpath to BIDS stats model.

--preproc_dir

Fullpath to the directory with the preprocessed data.

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--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

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

--boilerplate_only

When set to true this will only generate figures describing the raw data, the methods section boilerplate.

Default: False

--keep_residuals

Keep GLM residuals.

Default: False

--design_only

To only specify the GLM without estimating it.

Default: False

--use_dummy_regressor

If true any missing condition will be modelled

by a dummy regressor of NaN.

Default: False

--ignore

Possible choices: qa

To specify steps to skip.

--roi_based

Use to run a ROI-based analysis.

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.

--node_name

Model node to run.

--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

--roi_atlas

Possible choices: glasser, wang, neuromorphometrics, hcpex, anatomy_toobox, visfatlas

Atlas to create the regions of interest from.

Default: 'neuromorphometrics'

contrasts#

Compute contrasts and get results

bidspm contrasts [-h]
                 [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                 [--verbosity {0,1,2,3}] [--bids_filter_file BIDS_FILTER_FILE]
                 [--options OPTIONS] --model_file MODEL_FILE
                 [--preproc_dir PREPROC_DIR] [--task TASK [TASK ...]]
                 [--space SPACE [SPACE ...]] [--fwhm FWHM] [--dry_run]
                 [--skip_validation] [--boilerplate_only] [--concatenate]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--model_file

Fullpath to BIDS stats model.

--preproc_dir

Fullpath to the directory with the preprocessed data.

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--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

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

--boilerplate_only

When set to true this will only generate figures describing the raw data, the methods section boilerplate.

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

results#

Get results

bidspm results [-h]
               [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
               [--verbosity {0,1,2,3}] [--bids_filter_file BIDS_FILTER_FILE]
               [--options OPTIONS] --model_file MODEL_FILE
               [--preproc_dir PREPROC_DIR] [--task TASK [TASK ...]]
               [--space SPACE [SPACE ...]] [--fwhm FWHM] [--dry_run]
               [--skip_validation] [--boilerplate_only]
               [--roi_atlas {glasser,wang,neuromorphometrics,hcpex,anatomy_toobox,visfatlas}]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--model_file

Fullpath to BIDS stats model.

--preproc_dir

Fullpath to the directory with the preprocessed data.

--task

Tasks of the input data.

--space

Space of the input data.

Default: ['IXI549Space']

--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

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

--boilerplate_only

When set to true this will only generate figures describing the raw data, the methods section boilerplate.

Default: False

--roi_atlas

Possible choices: glasser, wang, neuromorphometrics, hcpex, anatomy_toobox, visfatlas

Atlas to create the regions of interest from.

Default: 'neuromorphometrics'

bms#

Run bayesian model selection

bidspm bms [-h]
           [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
           [--verbosity {0,1,2,3}] [--bids_filter_file BIDS_FILTER_FILE]
           [--options OPTIONS] --models_dir MODELS_DIR [--fwhm FWHM]
           [--dry_run] [--skip_validation]
Named Arguments#
--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'.

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--bids_filter_file

Fullpath to a JSON file describing custom BIDS input filters.

--options

Path to JSON file containing bidspm options.

--models_dir

Fullpath to the directory with the models.

--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

--dry_run

When set to true this will generate and save the SPM batches, but not actually run them.

Default: False

--skip_validation

To skip BIDS dataset and BIDS stats model validation.

Default: False

All parameters use snake_case. For a more readable version of this help section, see the online https://bidspm.readthedocs.io/en/latest/usage_notes.html.

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