I’m having issues normalizing a functional image to mni space for a subset of my participants. 4 out of 64 participants, all with the same scanning parameters, do not output files in mni space.
Their t1w images are fine. They get preprocessed and normalized and the warp field file gets created, but the final (preproc, mni sapce) functional image is where the problem occurs. The bold_space-mni_preproc file gets created but isn’t actually in mni space. What’s even odder is that the space-T1w_preproc image never actually gets created, which I believe is required for ANTs to normalize to mni space and output the final preproc image.
I found an old post indicating that old data in a working directory could be to blame, but I’ve re-run the participants using a new directory with the same outcome. I also included a verbose flag for one of the participants, but I don’t see any errors or anything to be concerned about really.
Ideally, I’d like to process everything in fmriprep, but I’m willing to preprocess up to registration/normalization, manually perform those tasks using ANTs, then perform ica-aroma. The only issue is that the preprocessed functional never gets written to the directory.
The jobs complete without throwing errors and the report doesn’t list anything either. I’m using fmriprep v1.1.4 with singularity on a cluster. The verbose logs don’t indicate that we’re exceeding the memory limit or anything, but could that be to blame? Is there a flag that I can include to halt fmriprep at the coregistration step so that I can manually perform the other steps?