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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Daniel Glen
April 12, 2010 11:11AM
You can use slice timing in NIFTI files, and NIFTI format files can end in ".hdr", ".nii" or ".nii.gz". Use nifti_tool to modify the dataset and change the slice_code field if you want. That field is described at this link:

[nifti.nimh.nih.gov]
[nifti.nimh.nih.gov]

But you really don't need to change or add a field if you specify the slice timing pattern with "-tpattern" to 3dTshift. 3drefit can modify the header information of AFNI format datasets to add or change slice timing information. See these previous links for more information:

[afni.nimh.nih.gov]
<[afni.nimh.nih.gov];
[afni.nimh.nih.gov]
<[afni.nimh.nih.gov];

Most AFNI commands work with NIFTI format, but not all of them (notably adwarp, align_epi_anat.py and a few others). You may be better off switching to AFNI format for part of the processing and switching back to NIFTI when you need it with 3dAFNItoNIFTI, 3dcopy or a NIFTI prefix with another command.
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Subject Author Posted

3dTshift -slice

Jian Lin April 09, 2010 10:15AM

Re: 3dTshift -slice

Ziad April 09, 2010 08:40PM

Re: 3dTshift -slice

Jian Lin April 12, 2010 09:44AM

Re: 3dTshift -slice

Daniel Glen April 12, 2010 11:11AM