We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Hard to tell. We do use 3dSkullStrip on T2 human data and it is OK for that, usually. For a rat T2, I can't tell and I can't tell if the absence of a spatial transform is the cause of the problem without more info. If the T2 volume looks OK in AFNI then the transform is not the problem. Have you tried to use the -visual option in 3dSkullStrip to determine what might be going awry?