Command Line Interface
cubids --help
This will print the instructions for using the command line interface in your command line.
usage: cubids [-h] [-v]
{validate,sidecar-merge,group,apply,purge,add-nifti-info,copy-exemplars,undo,datalad-save,print-metadata-fields,remove-metadata-fields}
...
Named Arguments
- -v, --version
show program’s version number and exit
Sub-commands
validate
cubids-validate: Wrapper around the official BIDS Validator
cubids validate [-h] [--sequential] [--container CONTAINER]
[--ignore_nifti_headers]
[--sequential-subjects SEQUENTIAL_SUBJECTS [SEQUENTIAL_SUBJECTS ...]]
bids_dir output_prefix
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
- output_prefix
file prefix to which tabulated validator output is written. If users pass in just a filename prefix e.g. V1, then CuBIDS will put the validation output in bids_dir/code/CuBIDS. If the user specifies a path (e.g. /Users/scovitz/BIDS/V1) then output files will go to the specified location.
Named Arguments
- --sequential
Run the BIDS validator sequentially on each subject.
Default: False
- --container
Docker image tag or Singularity image file.
- --ignore_nifti_headers
Disregard NIfTI header content during validation
Default: False
- --sequential-subjects
List: Filter the sequential run to only include the listed subjects. e.g. –sequential-subjects sub-01 sub-02 sub-03
sidecar-merge
bids-sidecar-merge: merge critical keys from one sidecar to another
cubids sidecar-merge [-h] from_json to_json
Positional Arguments
- from_json
Source json file.
- to_json
destination json. This file will have data from from_json copied into it.
group
cubids-group: find key and parameter groups in BIDS
cubids group [-h] [--container CONTAINER]
[--acq-group-level {subject,session}] [--config CONFIG]
bids_dir output_prefix
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
- output_prefix
file prefix to which a _summary.tsv, _files.tsv _AcqGrouping.tsv, and _AcqGroupInfo.txt, are written. If users pass in just a filename prefix e.g. V1, then CuBIDS will put the four grouping outputs in bids_dir/code/CuBIDS. If the user specifies a path (e.g. /Users/scovitz/BIDS/V1 then output files will go to the specified location.
Named Arguments
- --container
Docker image tag or Singularity image file.
- --acq-group-level
Possible choices: subject, session
Level at which acquisition groups are created options: ‘subject’ or ‘session’
Default: “subject”
- --config
Path to a config file for grouping. If not provided, then the default config file from CuBIDS will be used.
apply
cubids-apply: apply the changes specified in a tsv to a BIDS directory
cubids apply [-h] [--use-datalad] [--container CONTAINER]
[--acq-group-level {subject,session}] [--config CONFIG]
bids_dir edited_summary_tsv files_tsv new_tsv_prefix
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
- edited_summary_tsv
path to the _summary.tsv that has been edited in the MergeInto and RenameKeyGroup columns. If the summary table is located in the code/CuBIDS directory, then users can just pass the summary tsv filename instead of the full path to the tsv
- files_tsv
path to the _files.tsv that has been edited in the MergeInto and RenameKeyGroup columns. If the files table is located in the code/CuBIDS directory, then users can just pass the files tsv filename instead of the full path to the tsv
- new_tsv_prefix
file prefix for writing the post-apply grouping outputs. If users pass in just a filename prefix e.g. V2, then CuBIDS will put the four grouping outputs in bids_dir/code/CuBIDS. If the user specifies a path (e.g. /Users/scovitz/BIDS/V2 then output files will go to the specified location.
Named Arguments
- --use-datalad
ensure that there are no untracked changes before finding groups
Default: False
- --container
Docker image tag or Singularity image file.
- --acq-group-level
Possible choices: subject, session
Level at which acquisition groups are created options: ‘subject’ or ‘session’
Default: “subject”
- --config
Path to a config file for grouping. If not provided, then the default config file from CuBIDS will be used.
purge
cubids-purge: purge associations from the dataset
cubids purge [-h] [--use-datalad] [--container CONTAINER] bids_dir scans
Positional Arguments
- bids_dir
path to the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json.
- scans
path to the txt file of scans whose associations should be purged.
Named Arguments
- --use-datalad
ensure that there are no untracked changes before finding groups
Default: False
- --container
Docker image tag or Singularity image file.
add-nifti-info
cubids-add-nifti-info: Add information from niftifiles to the sidecars of each dataset
cubids add-nifti-info [-h] [--use-datalad] [--force-unlock]
[--container CONTAINER]
bids_dir
Positional Arguments
- bids_dir
absolute path to the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json.
Named Arguments
- --use-datalad
ensure that there are no untracked changes before finding groups
Default: False
- --force-unlock
unlock dataset before adding nifti info
Default: False
- --container
Docker image tag or Singularity image file.
copy-exemplars
cubids-copy-exemplars: create and save a directory with one subject from each Acquisition Group in the BIDS dataset
cubids copy-exemplars [-h] [--use-datalad] [--min-group-size MIN_GROUP_SIZE]
[--container CONTAINER]
bids_dir exemplars_dir exemplars_tsv
Positional Arguments
- bids_dir
path to the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json.
- exemplars_dir
absolute path to the root of a BIDS dataset containing one subject from each Acquisition Group. It should contain sub-X directories and dataset_description.json.
- exemplars_tsv
absolute path to the .tsv file that lists one subject from each Acquisition Group (*_AcqGrouping.tsv from the cubids-group output)
Named Arguments
- --use-datalad
check exemplar dataset into DataLad
Default: False
- --min-group-size
minimum number of subjects an Acquisition Group must have in order to be included in the exemplar dataset
Default: 1
- --container
Docker image tag or Singularity image file.
undo
cubids-undo: revert most recent commit
cubids undo [-h] [--container CONTAINER] bids_dir
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
Named Arguments
- --container
Docker image tag or Singularity image file.
datalad-save
cubids-datalad-save: perform a DataLad save on a BIDS directory
cubids datalad-save [-h] [-m M] [--container CONTAINER] bids_dir
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
Named Arguments
- -m
message for this commit
- --container
Docker image tag or Singularity image file.
print-metadata-fields
cubids-print-metadata-fields: print all unique metadata fields
cubids print-metadata-fields [-h] [--container CONTAINER] bids_dir
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
Named Arguments
- --container
Docker image tag or Singularity image file.
remove-metadata-fields
cubids-remove-metadata-fields: delete fields from metadata
cubids remove-metadata-fields [-h] [--fields FIELDS [FIELDS ...]]
[--container CONTAINER]
bids_dir
Positional Arguments
- bids_dir
the root of a BIDS dataset. It should contain sub-X directories and dataset_description.json
Named Arguments
- --fields
space-separated list of metadata fields to remove.
Default: []
- --container
Docker image tag or Singularity image file.