ASLPrep 25.1.0 using mri_coreg

matt.sherwood · October 16, 2025, 2:08pm

Summary of what happened:

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):

PASTE CODE HERE

Version:

25.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Docker pennlinc/aslprep version 25.1.0

Data formatted according to a validatable standard? Please provide the output of the validator:

![image|690x337](upload://n7CdkRwkaaqrcNnTEvo8jWe5OMt.jpeg)

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

tsalo · October 16, 2025, 4:03pm

Can you please include more information about your dataset, as well as the log files from your ASLPrep run?

matt.sherwood · October 16, 2025, 7:15pm

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.