Example BIDS File Names

The following examples assume there is a session, so each filename must include the session entity. To keep the list short, I have not included the JSON files. Note that while many key-value entities are common across different modalities, some entities are modality-specific.

anat

The anat directory contains structural scans. See the bids-specification: anatomy imaging data.
- sub-219_ses-itbs_T1w.nii.gz
- sub-219_ses-itbs_T2w.nii.gz

dwi

The dwi directory contains bvals and bvecs files in addition to the images.
- sub-219_ses-itbs_dir-AP_dwi.bval
- sub-219_ses-itbs_dir-AP_dwi.bvec
- sub-219_ses-itbs_dir-AP_dwi.json
- sub-219_ses-itbs_dir-AP_dwi.nii.gz

bvals and bvecs??

The contents of the BIDS bvals and bvecs are arranged in rows like FSL bvals and bvecs. See the bids-specification: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#diffusion-imaging-data

fmap

The fmap directory contains field maps and other files used for distortion correction (See the bids-specification: Fieldmap data)
- The magnitude and phasediff images are acquired as two separate DICOM series (the two magnitude images are in one, and the phasediff image is in the other). These are split into three NIfTI image files!
- Occasionally, you'll need to manually add a second EchoTime value to the phasediff JSON sidecar (this can depend on the DICOM to BIDS conversion tool you use)
  - sub-219_ses-itbs_phasediff.nii.gz
- It is acceptable for the sidecar to include EchoTime, EchoTime1 and EchoTime2
- EchoTime1 can be found in the magnitude1 JSON sidecar (it may be called EchoTime).
  - sub-219_ses-itbs_magnitude1.nii.gz
- EchoTime2 can be found in the magnitude2 JSON sidecar (it may be called EchoTime).
  - sub-219_ses-itbs_magnitude2.nii.gz
- The IntendedFor field may need to be added to the appropriate JSON sidecars in order to guarantee the companion image will be used for susceptibility distortion correction. Typically, the phasediff is intended for correcting bold images, though it can also be used to correct ASL images.
- If available, a reverse phase encoded (RPE) B0 image is used for susceptibility distortion correction of the DWI image. This RPE image is classified as modality "epi" (Technically, this RPE image is not a field map, but BIDS classifies it as field map because it is used for distortion correction).
  - sub-219_ses-itbs_dir-PA_epi.nii.gz

func

The func directory contains bold images and event text files. See the bids-specification: task imaging data if you want more details.
- sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
- sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
- sub-219_ses-itbs_task-rest_run-01_events.tsv
- sub-219_ses-itbs_task-rest_run-02_events.tsv

BIDS 2 (5 pts): How?