structural MR data: Naming conventions

The below is taken directly from the BIDS specification (version 1.1.1); please see this for full details. See 8.1.1. 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 structural images is as follows:

  • sub-<participant_label>/[ses-<session_label>/]
  •  ... anat/
  •   ... sub-<participant_label>[_ses-<session_label>][_acq-<label>][_ce <label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]

The following are the 'modality labels' for common image types. The example filenames, when given, are from those in our lab.

We do not use the session modifier for structural images. We have a single scan session in well over 90% of our cases, and in the few instances where we have longitudinal data we are focused on the functional data and typically use a single structural image as a reference.

Subset of keys – see spec. for full list.

Name Modality label Example
T1 weighted T1w sub-y0001_acq-mprage_run-01_T1w.nii.gz
T2 weighted T2w sub-y0001_acq-axtse_run-01_T2w.nii.gz
T2* T2star
FLASH FLASH sub-y0001_FLASH.nii.gz
Inplane T1 inplaneT1
Inplane T2 inplaneT2

'Acq' modifier: Sequence parameters

The OPTIONAL “acq-

'rec' modifier – reconstruction algorithms (e.g., moco)

Similarly the OPTIONAL “rec-

'Run' modifier – multiple acquisitions.

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). When there is only one scan of a given type the suffix MAY be omitted. As recommended in the conventions we zero-pad run number; i.e., run-01 not run-1.


Derived anatomical image naming conventions.

Separate to the above, in processing a series of derived images are created and need to be named. We store all basic derived anatomical images, which will be used in multiple different preprocessing streams, in-

  • derivatives / preproc_core / subj-[id] / ses-[id] / anat /

There is a proposal to include this as a future extension in the protocol. Where this is stored, however, is open to interpretation and it would be entirely appropriate to store this in the preprocessing folder for your pipeline, e.g.,

  • derivatives / preproc_[studyname] / subj-[id] / ses-[id] / anat /

Note that in deriving names, below, the base is always the name of the sourcefile, with additional variant information appended to the file name. When deriving switches, consult the common derivatives proposal and then test the altered output in your dataset with the BIDS validator.

Name Notes Example
Standard T1w sub-y0001_acq-mprage_run-01_T1w.nii.gz
Cropped T1w sub-y0001_acq-mprage_rec-crop_run-01_T1w.nii.gz
Origin corrected Not indicated. For now replace existing file.
Skull stripped T1w sub-y0001_acq-mprage_rec-crop_run-01_T1w_brain.nii.gz
T2w sub-y0001_acq-mprage_run-01_T2w_brain.nii.gz
Brain mask T1w sub-y0001_acq-mprage_rec-crop_run-01_T1w_brainmask.nii.gz
Segmentation grey sub-y0001_acq-mprage_rec-crop_run-01_T1w_greymatter.nii.gz
white sub-y0001_acq-mprage_rec-crop_run-01_T1w_whitematter.nii.gz
csf sub-y0001_acq-mprage_rec-crop_run-01_T1w_csf.nii.gz
Head-brain overlay T1w sub-y0001_acq-mprage_rec-crop_run-01_T1w_brain_overlay.nii.gz
MNI 152 space FSL mni152 sub-y0001_acq-mprage_rec-crop_run-01_T1w_space-MNI152NLin6Sym_var-fsl_preproc.nii.gz
ROI sub-y0001_acq-mprage_rec-crop_run-01_T1w_space-[space]_variant-[variant]_label-[label].nii.gz
  • Example file names were developed with reference to the preproc_common proposal.
  • Brainmask is binary; 1 inside brain, 0 outside brain. No NAN.
  • 'space' denotes the last template a given volum was coregistered to. T1w indicates native space. MNI152NLin6Sym is the MNI152 template used by FSL, and SPM99-SPM8. MNI152LIN is the version with linear coregistration.
  • When space is unspecified, native is assumed.
  • 'res' denotes the image resolution volumes have been resliced to, in mm (e.g., 1x1x1).
  • A standard set of keys for atlas names is being developed in the protocol, as linked above.
  • For ROI, 'variant' can reference different flavors (e.g., structural, functional, etc.).