Usage Notes

Command-Line Arguments

Creates a cohort by grabbing specific subjects from opennneuro datasets.

usage: cohort_creator [-h] [-v] {install,get,copy} ...

Positional Arguments

command

Possible choices: install, get, copy

Choose a subcommand

Named Arguments

-v, --version

show program’s version number and exit

Sub-commands

install

Install several openneuro datasets.

Example:

cohort_creator install \
    --datasets_listing inputs/datasets.tsv \
    --participants_listing inputs/participants.tsv \
    --output_dir outputs \
    --dataset_types raw mriqc fmriprep \
    --verbosity 3

cohort_creator install [-h] [-d DATASETS_LISTING] [-p PARTICIPANTS_LISTING]
                       [-o OUTPUT_DIR]
                       [--dataset_types {raw,mriqc,fmriprep} [{raw,mriqc,fmriprep} ...]]
                       [--verbosity {0,1,2,3}]

Named Arguments

-d, --datasets_listing

Path to TSV file containing the list of datasets to install.

-p, --participants_listing

Path to TSV file containing the list of participants to get.

-o, --output_dir

Fullpath to the directory where the output files will be stored.

--dataset_types

Possible choices: raw, mriqc, fmriprep

Dataset to install and get data from.

Default: [‘raw’]

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

get

Get specified data for a cohort of subjects.

Example:

cohort_creator get \
    --datasets_listing inputs/datasets.tsv \
    --participants_listing inputs/participants.tsv \
    --output_dir outputs \
    --dataset_types raw mriqc fmriprep \
    --datatype anat func \
    --space T1w MNI152NLin2009cAsym \
    --jobs 6 \
    --verbosity 3

cohort_creator get [-h] [-d DATASETS_LISTING] [-p PARTICIPANTS_LISTING]
                   [-o OUTPUT_DIR]
                   [--dataset_types {raw,mriqc,fmriprep} [{raw,mriqc,fmriprep} ...]]
                   [--verbosity {0,1,2,3}]
                   [--datatypes {anat,func} [{anat,func} ...]] [--space SPACE]
                   [--jobs JOBS]

Named Arguments

-d, --datasets_listing

Path to TSV file containing the list of datasets to install.

-p, --participants_listing

Path to TSV file containing the list of participants to get.

-o, --output_dir

Fullpath to the directory where the output files will be stored.

--dataset_types

Possible choices: raw, mriqc, fmriprep

Dataset to install and get data from.

Default: [‘raw’]

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--datatypes

Possible choices: anat, func

Datatype to get.

Default: [‘anat’]

--space

Space of the input data. Only applies when dataset_types requested includes fmriprep.

Default: “MNI152NLin2009cAsym”

--jobs

Number of jobs: passed to datalad to speed up getting files.

Default: 6

copy

Copy cohort of subjects into separate directory.

Example:

cohort_creator copy \
    --datasets_listing inputs/datasets.tsv \
    --participants_listing inputs/participants.tsv \
    --output_dir outputs \
    --dataset_types raw mriqc fmriprep \
    --datatype anat func \
    --space T1w MNI152NLin2009cAsym \
    --verbosity 3

cohort_creator copy [-h] [-d DATASETS_LISTING] [-p PARTICIPANTS_LISTING]
                    [-o OUTPUT_DIR]
                    [--dataset_types {raw,mriqc,fmriprep} [{raw,mriqc,fmriprep} ...]]
                    [--verbosity {0,1,2,3}]
                    [--datatypes {anat,func} [{anat,func} ...]]
                    [--space SPACE]

Named Arguments

-d, --datasets_listing

Path to TSV file containing the list of datasets to install.

-p, --participants_listing

Path to TSV file containing the list of participants to get.

-o, --output_dir

Fullpath to the directory where the output files will be stored.

--dataset_types

Possible choices: raw, mriqc, fmriprep

Dataset to install and get data from.

Default: [‘raw’]

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level.

Default: 2

--datatypes

Possible choices: anat, func

Datatype to get.

Default: [‘anat’]

--space

Space of the input data. Only applies when dataset_types requested includes fmriprep.

Default: “MNI152NLin2009cAsym”

For a more readable version of this help section, see the online doc https://cohort-creator.readthedocs.io/en/latest/