I am pre-processing some data for the first time that has already been collected. I have PAR/REC files and have tried to convert these using bidsify. While they are now converted into NIFTI and BIDS json sidecars they are still not in the BIDS compatible folder structure nor do they have the correct names. I am also unsure how to obtain phase diff and magnitude files from the B0 mapping PAR/REC file.
Any insight would be appreciated!
The Philips PAR/REC format is inherently concise and lacks much of the meta-data required for subsequent analyses. Therefore, you will have to look at the sequences on the scanner console to fill in a lot of the required information in the BIDS sidecar.
Be aware that a Philips scanner can save a Fieldmap in different forms, for example as a computed field map (in Hz), two pairs of magnitude and phase images, or as real and imaginary data. Inspecting the image_type_mr column in the PAR header (which is a simple text file) may help.
The FSL FUGUE web page provides information on how to proceed.