Michael Harms

@cmpetty Thanks for assembling this, but I think it needs a couple tweaks: 1. Did you test this in the context of the standard situation in which the TR_units are...

@coalsont Other than what I just mentioned above, do you see any other necessary changes to this PR, to resolve issue #124?

It’s the dwell time (interval between points in k-space in the *readout direction), expressed in seconds. See comments and notes in $HCPPIPEDIR/Examples/Scripts/PreFreeSurferPipelineBatch.sh -- Michael Harms, Ph.D. ----------------------------------------------------------- Associate Professor of...

While we are at it, we should also make sure that all `flirt` calls have a single 3D volume as the `-ref` volume, since `flirt` from FSL 6.0+ abends if...

A note regarding how the behavior of `bet` has changed as well _in the context of multi-frame input files_: **FSL5** - You get a single frame output, (unless you use...

Based on a quick look, this does appear to have changed more than I was anticipating. It looks like the batch script is itself being turned into another script that...

I'm afraid that this has turned into something much more complicated than I was envisioning when I proposed that we do something along the lines of just the following: ```...

While, in general, I'm not a fan of duplicating content into separate scripts (because then edits to one in the future have to propagated to both), perhaps this is a...

And we could duplicate all the variable related comments in both scripts, to make it easier to keep the scripts otherwise aligned, except where absolutely necessary to add info specific...

Regarding the jsons: I'm ok with us referring to them in some fashion, **but** we need to keep in mind that the generation of the sidecar json's (from `dcm2niix`) is...