@[toc](BRAIN IMAGING DATA STRUCTURE) # Links **The BIDS website**: [http://bids.neuroimaging.io/](http://bids.neuroimaging.io/) **The Brain Imaging Data Structure (BIDS) Specification:** [http://bids.neuroimaging.io/bids_spec1.0.1-rc1.pdf](http://bids.neuroimaging.io/bids_spec1.0.1-rc1.pdf) **Browse example datasets:** [https://github.com/INCF/BIDS-examples](https://github.com/INCF/BIDS-examples) **Download example datasets:** [https://drive.google.com/folderview?id=0B2JWN60ZLkgkMGlUY3B4MXZIZW8&usp=sharing](https://drive.google.com/folderview?id=0B2JWN60ZLkgkMGlUY3B4MXZIZW8&usp=sharing) **BIDS 2.0 - suggestions and changes that break backward compatibility:** [https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw/edit#](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw/edit#) # BIDS Apps [fmriprep: A Robust Preprocessing Pipeline for fMRI Data](http://fmriprep.readthedocs.io/en/stable/) # DSN Scripts [DSN github](https://github.com/dsnlab) `convert_bids` - convert to BIDS format and create file structure # BIDS for fileldmaps ## [LCNI fieldmaps](https://lcni.uoregon.edu/kb-articles/kb-0003) ### Method 1: Stock double-echo gradient echo field map (the "old" way) - Calculates a field map based on the difference in phase between two different echos in a double echo sequence. - You get 2 series, which contain: + Two magnitude images (one for each echo) + Single phase difference image (subtraction of the two phase images from each echo) - For this type of fieldmap, we want to use the template in Bids Specs section _"8.9.1 Case 1: Phase difference image and at least one magnitude image"_, page 22. ### Method 2: se-epi with opposite phase encode (the "new" way) - uses two separate acquisitions with opposite phase encoding directions to calculate a field map based on the difference in distortion between the two acquisitions. - You get 2 series, which contain: + Each contain a single magnitude volume with opposite phase encoding direction. - For this type of fieldmap, we want to use the template in Bids Specs section _"8.9.4 Case 4: Multiple phase encoded directions (topup)"_, page 25. ## Metadata needed for fieldmaps **Method 1:** - Echo Times of the two phase images used to create the difference image. **Method 2:** - Total readout time defined in seconds (FSL definition). - phase encoding direction. ### Fieldmap naming conventions `sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_mag nitude2.nii[.gz]`