*Note*
This question has been split into a separate thread from where it was originally asked (which was here: [afni.nimh.nih.gov]).

It is a separate question, so it should have its own thread. In the future, please address new questions with separate threads, for readability.

--pt

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Hi AFNI Experts,
I wanted to get some clarification on 3dQwarp and automask as well as the interaction -weight as I may have an issue as well. In the 3dQwarp -emask documentation it states the following:

The base image always automasked -- the emask is
extra, to indicate voxels you definitely DON'T want
included in the matching process, even if they are
inside the brain.


This suggests that the base image is always auto masked regardless of weight options as a first step. Since there is no way to pass a clip fraction I assume 3dAutomask with a default clip fraction of 0.4 is used. On my T2 image this seems to exclude most of the brainstem on a particular subject.

1) If I pass a custom weight image that includes the brainstem, would this brainstem area be used or skipped since the automask does not include the brainstem in this case? In other words, does the -weight option take precedence over the automatic use of automasking in 3dQwarp? Is the automasking only used as part of creating a weight in 3dQwarp or is the image itself actually masked prior to matching?

2) If the 3dAutomask is always used first, is it possible to expose a clip fraction parameter for us to adjust, as well as include a way to save the mask out for troubleshooting?

Thanks,
Ajay



Edited 1 time(s). Last edit at 12/30/2019 03:57PM by ptaylor.