Regarding the alignment (different brain shape after the pre-processing)

Dear AFNI experts,

I have an question regarding the alignment… (actually, I’m not fully sure that it is related to the alignment…)
Not all the subjects, but only one subject shows different brain shape after pre-processing.
(You could find the image in the attachment [(A): different one, (B) normal one].)

When I tried to check the step, it seems that it has an issue in ‘align’ part.
The problem is, even I tried to change the values or options,
(e.g. add option: -deoblique / change values in the options: -volreg off → -volreg on, 3dAutomask → 3dSkullStrip, and so on),
I could not get the correct one (I also tried to generate and input anatomical and epi data again).

Therefore, may I ask you how can I get the correct/general pre-processing result?
Thank you in advance.


Hi Dawoon,

It would be good to provide some actual commands that
you are using to process or otherwise register the
data. Is this with If so, what options
are you providing for registration (or what is the full

What does the EPI data look like? How do the EPI and
anat overlay in the first place?

  • rick

Dear rick,

Thank you for the comment.
I found that “-inweight -init_xform AUTO_CENTER” options in @auto_tlrc part could help to get correct shape of the brain.

Thank you :slight_smile: