Hi, Sahithyan-
This might be side issue in the processing to consider. Are you asking about the image QC_anatSS.514.jpg specifically? I think the oddness of the mask being truncated relates to the dataset not be centered around the coordinate origin (0,0,0). Given the displayed angle of the brain, I wonder if the input to SSwarper has obliquity in it?
We generally recommend deobliquing the anatomical before processing, to fit better into the alignment stream. Also, different software will deal with obliquity in different ways, so this removes some uncertainty and potential issues.
What is the output of the following, where DSET_ANAT is your anatomical volume input to SSwarper:
3dinfo -obliquity DSET_ANAT
?
If the output is not zero, then it would be preferable to get rid of the obliquity in a way not to interpolate the data, while also preserving the coordinate origin (we assume that that is actually reasonably well placed, when obliquity is considered). In very recent versions of AFNI, we have a new program called adjunct_deob_around_origin. In an older version of AFNI, you can just run:
3dcopy DSET_ANAT __tmp
3drefit oblique_recenter __tmp+orig
3drefit -deoblique __tmp+orig
3dcopy __tmp+orig DSET_ANAT_NEW
... where DSET_ANAT_NEW can be whatever output name you want. If you open that new dataset up in the AFNI GUI and jump to (x,y,z,)=(0,0,0), then hopefully you will see that coordinate origin location well-centered in the brain.
Also, we have recently added an updated version of @SSwarper called sswarper2 to the distribution, and you could also try using that instead of @SSwarper on the anatomical alignment, if you want. The options and output should be the same (just more QC images output) for integrating with afni_proc.py. But this is just if you want to try that.
--pt