Hi all,
We try as far as possible to avoid saving our processed fMRI images as new files after each step. My question is whether it is possible to combine the normalisation warp files with the results from sct_fmri_moco (e.g. …moco_x.nii.gz) into a single warp file. Nothing I’ve tried so far has worked.
By the way, the -dl function in sct_fmri_moco works very well! Great work!!
Best
Hanna
Hi @Hanna,
Thank you for your question! Just to make sure I’m understanding your needs correctly, what would you be planning to use the combined moco_x.nii.gz+moco_y.nii.gz file for?
For example, are you looking for the complete warping field to be used with e.g. sct_apply_transfo to be able to re-apply the motion correction transformation to another image?
(I ask because SCT has some prototype code for outputting a reusable warping field, and so understanding your use-case will help inform whether this would be helpful or not.)
Kind regards,
Joshua
Hi Joshua,
Yes, that’s exactly what I am trying to do. I tried to combine moco_x.nii.gz, moco_y.nii.gz, and other warp… nii.gz files for use in sct_apply_transfo.
Kind regards,
Hanna