I’m a little confused about output spaces of fMRIprep and would appreciate some clarification.
I have run fMRIprep (23.2.0) with the following output spaces: MNI152NLin2009cAsym, anat, fsnative.
In the derivatives/func directory, I now find both images with the label desc-coreg_boldref as well as the space-T1w_boldref label.
Indeed, the space-T1w_boldref image is aligned with the subject’s T1w image.
In contrast, the desc-coreg_boldref image is not aligned with T1w, but rather seems to be aligned with the original functional rawdata. I’m surprised, because I thought that the desc-coreg images are created for the BOLD-to-T1w registration. Is this not the case? Perhaps desc-coreg refers to suceptibility correction and head motion correction in the original functional space?
desc-hmc_boldref is a BOLD reference that is used as a target for head motion correction. desc-coreg_boldref is a BOLD reference that is used for coregistration. Both are in the original BOLD space, but they have had different things done to them to prepare them for these uses. These are obligatory derivatives.
space-T1w means the image has been actually resampled into the anatomical subject space. These are only created if you request outputs in this space.
If you’re interested, desc-coreg will start from an sbref rather than BOLD file, if available, and will be bias corrected to improve gray/white contrast and susceptibility distortion corrected to improve anatomical fidelity. If the sbref isn’t available, we start from desc-hmc_boldref and apply these steps.