As foretold in the 2018/05/30 Digest, the way that @SSwarper is run is now changing, in order to allow more generalized running (specifying output directory, unlimited variety of template targets, etc.). Note that the inner workings of the program have not changed, nor have its outputs files, nor has its method of integration into afni_proc.py. In summary: New look, same great taste!
As part of these changes, there are some new target templates for @SSwarper. The program @SSwarper uses a specific, multi-volume type of dataset to
be a target volume for its skullstripping+nonlinear registration. Traditionally, there was only one set for this (MNI152_2009_template.nii.gz); however, now this program has more generalized behavior, including the ability to use different reference volumes. We are therefore starting a new naming convention to denote
those special volumes, having “_SSW” after the prefix of the file name. This denotes the special 5-brick status of the given dataset.
At this time, two such data sets are now distributed with AFNI:
A) MNI152_2009_template_SSW.nii.gz, which used to be called MNI152_2009_template.nii.gz (the latter of which is now simply a
single volume, the th brick of the SSW dataset, a “normal” reference volume), and
B) TT_N27_SSW.nii.gz, which is the standard TT_N27 brain with supplementary volumes.
Some documentation about the 5-brick “SSW” volumes (and an example of how to make them, albeit in a slightly special case) is provided here:
For now, there are just these two (and interested users could write in with suggestions for other templates to be SSW-ized, as well).