Summary of what happened:
I’m trying to use my freesurfer subcortical segmentations to get a mask for my rs-fMRI. I used FreeSurfer’s mri_label2vol --regheader to move the seg into rawavg space (the original scanner space), which matched the fMRIPrep anatomical T1w dimensions (165×225×192, 1mm).
Then i did FSL resampling to BOLD space using FLIRT to get the segmentation from T1 to BOLD space (58×74×59, 2.4mm), but my labels disappeared/became too small to be useful (e.g. from 29 voxels to 2 voxels).
Now I’m thinking of trying the other way around, bringing the BOLD to the T1w - my thought process is this way I can retain the precise resolution I need for the smaller subcortical structures. Is this possible/if so, what is the best tool to use for this? ANTs, SPM12, something else?
Command used (and if a helper script was used, a link to the helper script or the command generated):
PASTE CODE HERE
Version:
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE