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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Leo Ai
October 28, 2009 03:56PM
Here is the exact command:

align_epi_anat.py -tlrc_anat ../0013/T1_at+tlrc -epi IRN-1_Masked+orig -epi_base 0 -anat_has_skull no -epi_strip None -suffix _al2T1 -epi2anat

It says it's version 1.25, but it seems to run with the "-resample off" option. If I understand correctly I need to run the following next:

3dAllineate -cubic -1Dmatrix_apply T1_al2T1_mat.aff12.1D -prefix IRN-1-aligned IRN-1_Masked+orig

After running this, I noticed that the pixel dimensions and image matrix did not normalize to that of the T1_at+tlrc. As a result the BOLD and T1 still doesn't actually align. Is it supposed to normalize or do I need to play with 3drefit in order to actually get things to line up?
Reply Quote
RSS
Subject Author Posted

Align BOLD to T1

Leo Ai October 28, 2009 01:02PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 01:10PM

Re: Align BOLD to T1

Leo Ai October 28, 2009 01:56PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 02:57PM

Re: Align BOLD to T1

Leo Ai October 28, 2009 03:56PM

Re: Align BOLD to T1

Daniel Glen October 28, 2009 04:47PM