Name
derivatives
phenotype
session
datatype
guts[location]_ses-[session]_task-[task].tsv
guts[location]_ses-[session]_task-[task].json
subject
session
datatype
sub-[subjectid]_ses-[session]_task-[task]_[extra-information].[extension]
sub-[subjectid]_ses-[session]_task-[task]_[extra-information].json
The BIDS structure consists of a phenotype folder, subject folders, and a derivative folder.
Phenotype folder
Subject folders
Derivatives folder
Name
derivatives
phenotype
sub-gutseur0001
sub-gutseur0002
gutseur_demographics.tsv
gutseur_demographics.json
gutseur_participation.tsv
gutseur_participation.json
This is what the 'first-level' of a data structure could look like. A phenotype folder and individual subject folders. Additionally, there is room for files with participant information.
Generally speaking, information about participants themselves (demographics) is placed in the demographics file, whereas information about participation (e.g., dates of sessions, sessions completed, etc.) is placed in a participation file.
Additionally, there is room for a derivatives folder.
Name
phenotype
ses-01
quest
gutseur_ses-01_task-iri.tsv
gutseur_ses-01_task-iri.json
gutseur_ses-01_task-sdq.tsv
gutseur_ses-01_task-sdq.json
sub-gutseur0001
Questionnaire data consists of a single file for each questionnaire with responses from all participants (group-level data) and is therefore placed in the phenotype folder. All questionnaires get a separate TSV file per session and an accompanying JSON file.
Name
derivatives
phenotype
ses-01
beh
gutseur_ses-01_task-sddt_desc-aggregated_events.tsv
gutseur_ses-01_task-sddt_desc-aggregated_events.json
sub-gutseur0001
ses-01
func
sub-gutseur0001_ses-01_task-fmrirest_bold.json
sub-gutseur0001_ses-01_task-fmrirest_bold.nii.gz
sub-gutseur0001_ses-01_task-sddt_run-01_bold.json
sub-gutseur0001_ses-01_task-sddt_run-01_bold.nii.gz
sub-gutseur0001_ses-01_task-sddt_run-01_events.tsv
sub-gutseur0001_ses-01_task-sddt_recording-ecg_physio.tsv.gz
sub-gutseur0001_ses-01_task-sddt_recording-ecg_physio.json
sub-gutseur0001_ses-01_task-sddt_recording-respiro_physio.tsv.gz
In the 'func' folder - nested within the subject folder - you can find subject-level task-based and resting-state fMRI data, including concurrent physiological recordings acquired during the fMRI session (e.g., heart rate, respiration recorded simultaneously with MRI).
Additionally, combined (aggregrated) and processed events files can be placed in the derivatives folder. See the 'derivatives' tab for more information about fmri preprocessing derivatives.
Name
derivatives
phenotype
ses-01
beh
gutseur_ses-01_task-gonogo_desc-aggregated_events.tsv
gutseur_ses-01_task-gonogo_desc-aggregated_events.json
sub-gutseur0001
ses-01
eeg
sub-gutseur0001_ses-01_task-gonogo_channels.tsv
sub-gutseur0001_ses-01_task-gonogo_events.tsv
sub-gutseur0001_ses-01_task-gonogo_eeg.edf
sub-gutseur0001_ses-01_task-gonogo_eeg.json
In the 'eeg' folder - nested within the subject folder - you can find subject-level task-based and resting-state EEG data.
Additionally, combined (aggregrated) and processed events files can be placed in the derivatives folder. See the 'derivatives' tab for more information about preprocessing derivatives.
Name
phenotype
ses-01
beh
gutseur_ses-01_task-raven.tsv
gutseur_ses-01_task-raven.json
sub-gutseur0001
ses-01
beh
sub-gutseur0001_ses-01_task-socialeffort_beh.tsv
sub-gutseur0001_ses-01_task-socialeffort_beh.json
The location of behavioral data depends on how and when the data was collected:
- Group-level behavioral data, such as tasks administered through Qualtrics (e.g., the Raven task), are typically exported as a single file containing all participants. These should be placed in the
phenotype/beh/
folder. - Individual-level behavioral data, such as those generated by E-Prime or other computer tasks producing trial-by-trial outputs per participant, should be placed in each participant’s
beh/
folder within the subject directories. - If a behavioral task was performed during neuroimaging or EEG acquisition, the associated data should be stored in events files in the corresponding
func/
oreeg/
folders, not inbeh/
. - The
beh/
folder is reserved for behavioral or physiological tasks that were conducted independently of any concurrent neuro-recordings. - Additionally, combined (aggregrated) and processed _beh files can be placed in the derivatives folder. See the 'derivatives' tab for more information about preprocessing derivatives.
Name
sub-gutseur0001
ses-01
beh
sub-gutseur0001_ses-01_task-self_recording-ecg_channels.tsv
sub-gutseur0001_ses-01_task-self_recording-ecg_ecg.set
sub-gutseur0001_ses-01_task-self_recording-ecg_ecg.json
func
sub-gutseur0001_ses-01_task-sddt_recording-ecg_physio.tsv.gz
sub-gutseur0001_ses-01_task-sddt_recording-ecg_physio.json
sub-gutseur0001_ses-01_task-sddt_recording-respiro_physio.tsv.gz
The location of ECG - but also Respirometer and Skin conductance - data depends on the concurrent task that was measured.
For example, ECG data collected during an fMRI task will be placed in the 'func' folder, whereas ECG data collected during a computer task will be placed in the individual 'beh' folder.
Name
phenotype
ses-01
biosample
gutseur_ses-01_task-salivacort.tsv
gutseur_ses-01_task-salivacort.json
gutseur_ses-01_task-salivatesto.tsv
gutseur_ses-01_task-salivatesto.json
sub-gutseur0001
Hormone analysis output will consist of one file per measure that includes data of all participants and will therefore be placed in the ‘biosample’ folder in phenotype as it's at the group level. Additionally, equal to all other TSV files, an accompanying JSON file will be placed in the same folder for each file.
Name
derivatives
phenotype
ses-01
quest
gutseur_ses-01_task-iri_desc-totalscores.tsv
beh
gutseur_ses-01_task-socialeffort_desc-aggregated_beh.tsv
gutseur_ses-01_task-sddt_desc-aggregated_events.tsv
fmriprep
freesurfer
sub-gutseur0001
ses-01
surf
stats
mri
group
ses-01
gutseur_ses-01_task-smri_desc-freesurfer-corticalvol.tsv
gutseur_ses-01_task-smri_desc-freesurfer-corticalthickness.tsv
phenotype
sub-gutseur0001
The derivatives
folder is used to store files that result from data processed through a specific pipeline. It typically contains:
1. Pipeline-specific folders
2. A phenotype folder
Examples of files to include in the phenotype
folder are:
- Computed total or subscale scores from questionnaires or behavioral tasks
- Aggregated behavioral data
- use_beh
for data that’s not time-locked to the imaging data
- use_event
for time-locked events during an fMRI or EEG task. - Manually created group-level neurobiological files derived from Freesurfer output.
Alternatively, these neurobiological group-level files can be placed in a
group
subfolder within the appropriate pipeline folder, keeping all related pipeline output together. The
desc
field stands for description and should indicate what kind of data was derived from the original input. For example, it may describe data derived from sMRI via Freesurfer, or from a specific questionnaire like the IRI. Details about the original file should always be included in the accompanying JSON sidecar. Ensure that task information is included in the derivative file structure. Ideally, this should be embedded in the file name, for example:
sub-gutseur0001_ses-01_task-sddt_desc-brain_mask.nii.gz
If including task information in the filename isn’t possible, it must be reflected in the pipeline name, such as:
fmriprep_task-sddt