I am using ASLPrep version 25.1.0 after running fMRIPrep. With this I am reusing the freesurfer output produced from fmriprep where I forced bbr. When inspecting ASLPrep after upgrading to version 25.1.0 and re-running my data, coregistration is extremely poor. Looking at the reports, it is using mri_coreg but all the examples I can find show it should be using FLIRT. My command is in the image below. Any help in this would be great as I have tried multiple different inputs to aslprep and I continue to get poor registration when 0.7.5 produced acceptable registration for the same data.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Ok so I have 11 ASL scans per person collected from a Philips MRI. I have many studies that utilized this same acquisition and recently changed over from version 0.7.5 to 25.1.0. They are single-delay pcASL scans (GRASE) with 2 M0 volumes collected first followed by 5 tag-control pairs. The 11 scans were completed across 7 different sessions - 5 on the first and 1 on each session after the first. Each session also has a single T1w that was fed into fmriprep to compute a single subject template which was processed in freesurfer. Let me know if there are any specifics.
Registration is super poor in every dataset since transitioning to 25.1.0 and I can’t seem to find why it is using mri_coreg versus FLIRT. Attached is an example (a little more extreme). Not quite sure how to put the logfile in here as an attachment.
That is very odd. In the axial view, the coregistration looks okay to me, but obviously something’s wrong in the z dimension. Any chance you can share the raw data with me? E.g., by uploading to Box and DMing me the link.
