Is this similar to what mrgrid achieves?
mrgrid would take image data stored on one voxel grid, and resample it onto a different voxel grid. Where the target voxel grid is of higher spatial resolution than the input, the result will be “blurry”. With
5ttgen hsvs, anything with a surface-based representation (whether native or intermediate) can be mapped to a partial volume image on any target voxel grid. So even if the target voxel grid is of absurdly high spatial resolution, the partial volume image will still be exceptionally sharp, reflecting the infinitessimally thin nature of the surface-based representation.
While preprocessing DWI data I have used
epi_reg outside of mrtrix for fieldmap correction (reason being that some of our data only have gradient field maps as phase/magnitude pair). In my understanding epi_reg does both transformation and resampling onto higher resolution freesurfer T1 image which I have used as a reference image, but please correct me if I am wrong. I had to tend to epi_reg given the limitation of our dataset for EPI distortion correction. I believe resampling it back to lower-resolution might involve add-on interpolation which would be better off avoided, but open to better solutions.
While I head of
epi_reg regularly I’m not familiar with its operation. If this is the case it’s probably more justification to finally get around to supporting field maps in
dwifslpreproc; it just keeps getting bumped down the priority list because I don’t have any such data myself, so if anyone feels like getting their hands dirty with some Python please do…
Another related question I have is if
5ttgen hsvs can be used when we are using
samseg routine instead of
recon-all -all option?
If it doesn’t overwrite the standard FreeSurfer output files but instead creates its own with different names, then no,
hsvs won’t identify them. I’d not heard of it until now, so I’d need to see what it produces and whether or not it can be used.