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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pstchan
September 10, 2014 01:19AM
Hi,

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 as follows:

3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al anat_fs.nii

3dcalc -a anat_fs.nii -expr a -prefix anat_fs

3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al anat_fs+orig

The 'anat_fs_al+orig' output from 'anat_fs+orig' always aligns properly with the target dataset, while the output from 'anat_fs.nii' does not.

Any suggestion?

Thanks,
Phoebe
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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