functional MR data: Naming conventions

The below is taken directly from the BIDS specification (version 1.1.1); please see this for full details. See 8.3.3. CAPS words have proscribed meanings, as detailed in the specification. Note that most of these images are optional, but when included they should be named consistent with the conventions.

The basic template for the labeling a patient's functional images is as follows:

  • sub-<participant_label>/[ses-<session_label>/]
  •  ... func/
  •   ... sub-<participant_label>[_ses-<session_label>][_task-<task>][_acq-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]

Switches we use include the following.

Switch Values Example
Task Object naming sub-y0001_ses-mri01_task-1obj_acq-eng_run-01_bold.nii.gz
VRN sub-y0001_ses-mri01_task-2vrn_lang-eng_run-01_bold.nii.gz
ARN sub-y0001_ses-mri01_task-3arn_acq-eng_run-01_bold.nii.gz
Binder sub-y0001_ses-mri01_task-4bin_acq-eng_run-01_bold.nii.gz
Rest sub-y0001_ses-mri01_task-rest_acq-eng_run-01_bold.nii.gz
Language English sub-y0001_ses-mri01_task-1obj_acq-eng_run-01_bold.nii.gz
Farsi sub-y0001_ses-mri01_task-1obj_acq-far_run-01_bold.nii.gz
Greek sub-y0001_ses-mri01_task-1obj_acq-grk_run-01_bold.nii.gz
Hindi sub-y0001_ses-mri01_task-1obj_acq-hin_run-01_bold.nii.gz
Korean sub-y0001_ses-mri01_task-1obj_acq-kor_run-01_bold.nii.gz
Polish sub-y0001_ses-mri01_task-1obj_acq-pol_run-01_bold.nii.gz
Spanish-Sth Am. sub-y0001_ses-mri01_task-1obj_acq-ssa_run-01_bold.nii.gz
Spanish-European. sub-y0001_ses-mri01_task-1obj_acq-seu_run-01_bold.nii.gz
Portuguese-European. sub-y0001_ses-mri01_task-1obj_acq-peu_run-01_bold.nii.gz
Run 1 sub-y0001_ses-mri01_acq-1obj_acq-peu_run-01_bold.nii.gz

Per the specification:

  • Task. 'Each task has a unique label MUST only include of letters and/or numbers (other characters including spaces and underscores are not allowed). Those labels MUST be consistent across subjects and sessions.
  • Acq. 'The OPTIONAL “acq-
  • Rec. Similarly the optional “rec-
  • Run. If several scans of the same modality are acquired they MUST be indexed with a suffix: _run-1, _run-2, _run-3 etc. (only integers are allowed as run labels). In the context of functional imaging a run is defined as the same task, but in some cases it can mean different set of stimuli (for example randomized order) and participant responses.' As recommended in the conventions we zero-pad run number; i.e., run-01 not run-1.

Note also, multi-echo data is treated differently (see specification), and a paired JSON file is required. The metadata in the file contains a number of required fields.


Preprocessed data

Type SPM BIDS mod Nb. Source
realigned r- [source_file]_space-meanBOLD BEP003
coregistered r- [source_file]_space-T1w BEP003
smoothed s- _ BEP003
normalized w- [source_file]_space-MNI152NLin6Sym_var-fsl ¡ BEP003

¡ Note: We use var-fsl to indicate created in fsl.


Type Standard BIDS mod Nb. Source
ART regressors art_... [source_file]_confounds.tsv BEP012
xfm matrix [source_file]_target-[target]_variant-[label]_affine.txt Variant switch optional BEP014