AFNI Message Board

Dear AFNI users-

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.

Sincerely, AFNI HQ

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Adam Schwarz
January 31, 2008 04:32PM
Dear Experts,

I am using 3dAllineate to
(a) compute the transformation of an image volume B to its accompanying anatomical A (same bat-subject, same bat-session), then
(b) apply this transformation to a second image volume C, originally aligned with B.

Step (a) works well, but the output of step (b) results in C.reg having the top half of the brain chopped off. I\'m sure I\'m missing some little trick - could any kind soul illuminate for me?

The syntax I am using is:

3dAllineate -base A+orig \\
-1Dmatrix_save epi2anat.aff9.1D \\
-mi \\
-warp shift_rotate_scale \\
-prefix B.reg \\
-input B+orig

3dAllineate -1Dmatrix_apply epi2anat.aff9.1D \\
-warp shift_rotate_scale \\
-prefix C.reg \\
-master A+orig \\
-input C+orig

Many thanks in advance,
adam
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Subject Author Posted

3dAllineate

Adam Schwarz January 31, 2008 04:32PM

Re: 3dAllineate

Daniel Glen January 31, 2008 05:08PM