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.
Other
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 |