Josh

Notes on how dcm2niix handles PAR/REC sequences are here. Note that the PAR header can index images in a different order than they are stored in the REC file. I suspect if you look at your PAR files carefully you will see that dcm2niix is reordering them as directed in the PAR header. However, I believe this order is arbitrary, and may reflect details like when a volume was completed by reconstructors that were running in parallel with no bearing on true acquisition order.

Sample datasets demonstrate that the order that images are stored to disk and described in the PAR header do not reflect actual acquisition order. Ideally, it would be great if we could save these images in the same order as they were acquired (see Jesper Andersson's comments for issue 201). However, this is currently impossible with Philips PAR/REC data.

If possible, I would recommend you export the data to DICOM rather than PAR/REC format. I have tried to handle all the Philips PAR/REC data I have seen, but I do not have Philips equipment and there might be corner cases I am not aware of. I would suggest you acquire validation data as described in the 'dedicated document' on the dcm2niix wiki.