Filenames
Contents
Filenames¶
BIDS has a standardized way of naming files that tries to implement the following principles:
Do not include white spaces in file names
They make scripting harder.
Use only letters, numbers, hyphens, and underscores.
Some operating systems cannot handle special characters.
Do not rely on letter case (
UPPERCASE
andlowercase
)For some operating systems
a
is the same asA
.
Use separators and case in a systematic and meaningful way.
Source: Datalad RDM course
Filename template¶
key1 - value1 _ key2 - value2 _ suffix .extension
- Suffixes are preceded by an underscore
- Entities are composed of key-value pairs separated by underscores
- There is a limited set of suffixes for each data type (anat, func, eeg, …)
- For a given suffix, some entities are required and some others are [optional].
- Keys, value and suffixes can only contain letters and/or numbers.
- Entity key-value pairs have a specific order in which they must appear in filename.
- Some entities key-value can only be used for derivative data.
Modalities¶
MRI¶
anat
: Anatomical MRI data¶
myProject/sub-01/ses-01/anat/
- Data:
- `sub-<>[_ses-<>]_T1w.nii.gz`
- Metadata:
- `sub-<>[_ses-<>]_T1w.json`
func
: Functional MRI data¶
myProject/sub-01/ses-01/func/
- Data:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_bold.nii.gz`
- Metadata:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_bold.json`
- Events:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_events.tsv`
fmap
: Fieldmap MRI data¶
myProject/sub-01/ses-01/fmap/
- Data:
- `sub-<>_ses-<>_acq-<>_run-<>_phasediff.nii.gz`
- `sub-<>_ses-<>_acq-<>_run-<>_magnitude1.nii.gz`
- Metadata:
- `sub-<>_ses-<>_acq-<>_run-<>_phasediff.json`
dwi
: Diffusion Weighted Imaging data¶
myProject/sub-01/ses-01/dwi/
- Data:
- `sub-<>_ses-<>_acq-<>_run-<>_dwi.nii.gz`
- `sub-<>_ses-<>_acq-<>_run-<>_dwi.bval`
- `sub-<>_ses-<>_acq-<>_run-<>_dwi.bvec`
- Metadata:
- `sub-<>_ses-<>_acq-<>_run-<>_dwi.json`
EEG / MEG / iEEG¶
meg
: MEG data¶
myProject/sub-01/ses-01/meg/
- Data:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_proc-<>_meg.extension`
- Metadata:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_proc-<>_meg.json`
- Channel information:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_proc-<>_channels.tsv`
- Events:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_proc-<>_events.tsv`
- Sensor positions:
- `sub-<>_ses-<>_acq-<>_photo.jpg`
- `sub-<>_ses-<>_acq-<>_fid.json`
- `sub-<>_ses-<>_acq-<>_fidinfo.txt`
- `sub-<>_ses-<>_acq-<>_headshape.extension`
ieeg
: Intracranial EEG data¶
myProject/sub-01/ses-01/ieeg/
- Data:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_ieeg.extension`
- Metadata:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_ieeg.json`
- Channel information:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_channels.tsv`
- Events:
- `sub-<>_ses-<>_task-<>_acq-<>_run-<>_events.tsv`
- Electrode locations:
- `sub-<>_ses-<>_acq-<>_electrodes.tsv` _electrode xyz coordinates_
- `sub-<>_ses-<>_acq-<>_coordsystem.json` _coordinate metadata_
- `sub-<>_ses-<>_acq-<>_photo.jpg` _operative photo_