Dear experts,

I am using dcm2niix for my MRI data. However, I am uncertain about the value or necessity of using a so-called ' scaling factor'. I have noticed that dcm2bids (which I use), does not offer the freedom of choosing whether to incorporate the scaling factor or not, there are standard settings that always include the scaling factor. Now my question is, what this scaling factor does, as the data obviously changes their value after applying a scaling factor. This is also supported by my post-processing analyses.

Thanks for your time and advice.

Kind regards,
Julia Pottkaemper

You do not provide a lot of context, but I assume that you are referring to the way images from Philips scanners provide multiple mutually exclusive ways of converting the raw integer data saved to disk to floating point values. This is describe here:
  https://github.com/rordenlab/dcm2niix/tree/master/Philips#image-scaling
For most MRI modalities (T1, T2, fMRI T2*) the image intensity is relative, so these modifications have no impact (a higher scaling factor increases both the signal and noise, so general linear model statistical tests will be unchanged as they compute the ratio of explained signal to unexplained noise). For ASL the image intensity IS calibrated, and different processing tools make different assumptions (https://www.ncbi.nlm.nih.gov/pmc/article...). Therefore, your choice will depend on the tools you wish to use. For further details, contact the Philips Clinical Scientist associated with your instrument.