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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Peter Molfese
September 28, 2017 11:58AM
That's correct, 3dTshift does not know the slice order if they aren't transcribed into the header. This is actually pretty common with conversion of DICOMs to NIFTI via dcm2nii or other tools.

You should use the syntax for explicitly setting the slice order, just make sure to use the correct order: 

-tshift_opts_ts -tpattern seq-z

Alternatively, you can set the slice order using 3dTcat (-tpattern) or 3drefit. But I usually specify the order by hand in my afni_proc.py commands.
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Subject Author Posted

3dTshift: Does AFNI know the slice timing order?

Robin September 28, 2017 10:23AM

Re: 3dTshift: Does AFNI know the slice timing order?

Peter Molfese September 28, 2017 11:58AM

Re: 3dTshift: Does AFNI know the slice timing order?

Daniel Glen September 29, 2017 04:56PM

Re: 3dTshift: Does AFNI know the slice timing order? Attachments

Robin November 16, 2017 05:14AM

Re: 3dTshift: Does AFNI know the slice timing order?

Daniel Glen November 16, 2017 12:21PM

Re: 3dTshift: Does AFNI know the slice timing order?

Robin November 16, 2017 12:36PM

Re: 3dTshift: Does AFNI know the slice timing order?

Daniel Glen November 16, 2017 01:42PM

Re: 3dTshift: Does AFNI know the slice timing order? Attachments

Robin November 17, 2017 04:01AM

Re: 3dTshift: Does AFNI know the slice timing order?

rick reynolds November 17, 2017 09:03AM

Re: 3dTshift: Does AFNI know the slice timing order?

Robin November 17, 2017 09:37AM