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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nick
September 10, 2014 10:13AM
pstchan Wrote:
-------------------------------------------------------
> When I apply '3dAllineate' or 'align_epi_anat.py'
> to align a T1 anatomical dataset, I find a
> difference in the output for the same input
> dataset in NIFTI and BRIK format

AFNI can store additional transformations in the fields

- ALLINEATE_MATVEC_B2S_000000
- ALLINEATE_MATVEC_S2B_000000
- WARPDRIVE_MATVEC_FOR_000000
- WARPDRIVE_MATVEC_INV_000000

which is probably what is happening here (you can view the .HEAD file in a text editor to verify this). When loading AFNI files in the viewer, the transformation in these fields is used to map voxel indices to world coordinates. My guess is that when storing the output as NIFTI these fields are ignored.
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Subject Author Posted

NIFTI vs BRIK

pstchan September 10, 2014 01:19AM

Re: NIFTI vs BRIK

nick September 10, 2014 10:13AM

Re: NIFTI vs BRIK

Daniel Glen September 10, 2014 12:05PM

Re: NIFTI vs BRIK

pstchan September 10, 2014 05:41PM

Re: NIFTI vs BRIK

pstchan September 11, 2014 12:43AM

Re: NIFTI vs BRIK

Daniel Glen September 11, 2014 03:58PM