I’m new to fMRIprep. I’ve been working on a dataset recently and found some weird output from .html report. Particularly in ’ Alignment of functional and anatomical MRI data (surface driven)’ Session. The ‘fixed’ and ‘moving’ images are not overlaid well. I paste two screenshots for a sample participant. This issue is found in 3-4 participants in a 50 participants datasets. Please let me know if it is helpful to upload any source files or original T1 images. I wonder if this issue is related to bad T1? Should I change to other alignment method?
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS-validated
Relevant log outputs (up to 20 lines):
bbregister was used to generate transformations from EPI-space to T1w-space. Note that Nearest Neighbor interpolation is used in the reportlets in order to highlight potential spin-history and other artifacts, whereas final images are resampled using Lanczos interpolation.
I would try with just --bold2t1w-dof 6 before resorting to assuming the images are already mostly aligned with --bold2t1w-init header. The additional 3 degrees of freedom in 9-dof registration are scale factors, so they would presumptively cause the shrinking.
Also, did you get any Susceptibility Distorsion Correction done by fmriprep? i.e. do you provide fieldmaps in your dataset? This could help the registration also.
Hi @jsein , thanks for the suggestion! I’ll try that option and updated what I got. And to answer your question regarding the SDC. Yes, I have done SDC based on field map, and I attached the report here. Do you think it looks reasonable? I have some issues when I use the newest version of fmriprep (23.1.4), but it is solved using the current version I used now (21.0.1). I’ll post another issue regarding this, but it is less relevant to the current issue.
Hi, @Steven. Thanks! But I actually encountered serious issue with SDC when I’m using the newest release (Both 23.1.3 and 23.1.4). I solved this issue by changing the version back to 21.0.1. Due to this issue, I’m not able to run things correctly using the newest release. If anyone is interested in this issue, I’ll start another post about this.
Hi @KeBo2023 , About SDC, you could try fmriprep v23.2.0a3 for which SDC is expected to work better. But it would be interesting to understand why SDC was working for 21.0.1 and not for 23.1.4.
It would be important to know if it was a bug in the execution (the execution failed) or if it was the result that was wrong.
From the images you show, the image after SDC correction looks very reasonable, so I don’t thing the problem with realignment is coming from there. Let us know if the suggestions we made did change anything in the result.
Another possibility would be to not use bbregister for registration, but usually this is for cases where the GM/WM contrast in the functional image is very low which doesn’t look to be the case for your images. In that case, it is possible to use: --force-no-bbr.