option in AP for a mean functional output?

Feature Requests and Code Discussions
1

good day, Rick-

edge case request here, but i don't think it would be too hard to do. i find as i test high resolution EPIs that sometimes when i don't align an anatomical, the vr_base as underlay doesn't have quite enough SNR. i then manually go into .results and take a mean of the pb*volreg image for a nicer underlay. could there be an option added to AP that allows us to toggle this on (off by default)? feel free to put this at the bottom of your to-do list! and thanks for considering

-Sam

2

I'm not completely sure of what you want to do, but would the "-volreg_base_dset" option work with the output of 3dTstat or 3dvolreg/3dTstat to get the mean? There's also the -align_epi_ext_dset option that might help if doing this in combination with alignment to an anatomical dataset.

3

hey Daniel!

those options are about specifying different inputs to AP; i'm talking about an AP option that makes another little output file; essentially another vr_base but with higher SNR because it's not a single extracted volume but rather an average across the (already aligned) time series.

is that more clear? sorry if i was unclear before.

-Sam

4

So just for display then. Do you mean something like:

3dTstat -mean -prefix vr_r01_mean pb02.FT.r01.volreg+tlrc

Do you want that looped over all runs?

5

Yeah that's what I've been doing manually for years after APs finish. Some of these submillimeter functional scans are pretty grainy, although I can easily imagine this being useful to any low-snr sequence if others want to view results directly on functionals. As far as looping over runs, nah, it's diminishing returns in terms of SNR improvement. I think just an average across whatever run the vr_base comes from. Really appreciate you considering this!