fMRIPrep - discrepancy between coregistration displayed in the HTML report vs image comparison

Software Support
1

fMRIPrep runs just fine, and the HTML report suggests an acceptable coregistration has occurred:

image
image583×666 122 KB

But if I decide to plot the <session>/func/*_desc-coreg_boldref.nii.gz image against the /anat/*_desc-preproc_T1w.nii.gz, the images are not coregistered:

image

It’s not until I actually apply the transformation matrix located at <session>/anat/*_xfm.txt that the two aforementioned images actually become aligned:

image

Is the description coreg actually appropriate then if the image is not coregistered to the T1w image after all? Or was the transformation supposed to be applied? The current description in the docs:

Registration of the BOLD series to the T1w image generates a further reference image and affine transform

implies that this <session>/func/*_desc-coreg_boldref.nii.gz is coregistered to the T1w image.

2

It’s the image used to coregister to the T1w. If you want a boldref image that is coregistered to the T1w, you’ll want one with space-T1w in the filename.

3

Thanks! Appreciate the clarification. Marked as solved.

1 Like
4

The purpose is to distinguish it from desc-hmc_boldref.nii.gz, which is the reference used to perform HMC, as desc-coreg is used to perform coregistration. This has seemed to cause confusion, so I would be happy to consider a different name from desc-coreg_boldref.nii.gz.