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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
Group-level data files that are not specific to any particular neuroimaging modality, such as questionnaires or hormone level output. A single phenotype data file typically contains group-level data, with one row per participant, meaning all participants are included in a single file.
  • quest – Questionnaire data
  • beh – Behavioral task data aggregated at participant level (e.g., task scores from Qualtrics)
  • biosample – Biosample data (e.g., hormone levels)
Subject folders
Each subject folder contains data specific to that participant's recording sessions, organized by modality:
  • anat– Structural MRI data (e.g., T1w, T2w)
  • func– Task-based and resting-state fMRI data, including concurrent physiological recordings acquired during the fMRI scan (e.g., heart rate, respiration recorded simultaneously with the MRI).
  • eeg – Task-based and resting-state EEG data, including concurrent physiological recordings acquired during EEG.
  • beh – Individual task data and physiological recordings acquired independently of any neuroimaging or other modality recordings (e.g., ECG or skin conductance recorded outside the scanner, or trial-level behavioral data from computer tasks).
Derivatives folder
Contains processed or derived data based on the curated contents of the subject folders and the phenotype folder.
  • Processed and preprocessed neuroimaging data (excluding initial anonymization steps such as defacing)
  • Aggregated individual behavioral data, such as combined files from sub-*/beh/
  • Derived group-level measures, such as computed sum scores from questionnaires

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/ or eeg/ folders, not in beh/.

  • 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