Hi, Robin-

Why does the follower look weird here? I think it has to do with having an oblique input to SSW and using that "deoblique" opt.

What is obliquity? You see your data and it looks ~nicely aligned with axial slices in places we would expect to see them, so we can recognize the parts of the brain easily, BUT there is an additional matrix stored in the header to apply to the data to put it back into "scanner coords" (i.e., where the brain was in 'scanner space' when acquired). There are 2 ways to "deoblique" the dataset:
+ the 3drefit way: *purge* the obliquity transformation from the header, and pretend like it never existed. This would be like pretending your subject's head was in a different (and probably preferable, from a viewing standpoint) location/angle when the data was aquired-- namely, the location that it appears to be at present. The image you see in the AFNI GUI doesn't change in this deobliquing case: we now treat the oblique coords as if they were the scanner coords.
+ the 3dWarp way: *apply* the obliquity matrix to the dataset to put it into scanner coords. In this case the dataset gets resampled/regridded, and the appearance of the brain in the GUI will likely change-- it might be rotated/shifted. This dataset is now back in the scanner coords.

There are two opts in @SSwarper for dealing with obliquity, if you wish (but it's not necessary often to use one), one for each of the above, and they are here:

-deoblique :(opt) apply obliquity information to deoblique the input
              volume ('3dWarp -deoblique -wsinc5 ...'), as an initial step.
              This might introduce the need to overcome a large rotation
              during the alignment, though!

  -deoblique_refitly :(opt) purge obliquity information to deoblique
              the input volume (copy, and then '3drefit -deoblique ...'), 
              as an initial step.  This might help when data sets are
              very... oblique.

You chose "-deoblique", which is the 3dWarp-way, which resamples the dset before performing alignment, so your input T1w volume and the volume actually aligned to the template are in different spots-- that is why having your T1w as follower failed. You could use either "-deoblique_refitly" or no deobliquing to be able to have the T1w vol follow along.

--pt



Edited 2 time(s). Last edit at 02/24/2020 10:02AM by ptaylor.