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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lisam
October 09, 2014 12:34PM
Dear AFNI gurus,

I am analyzing data from a rapid event-related design, and I’m trying to figure out how to properly apply slice timing correction. I scanned on a Siemens 3T Trio that collects 42 slices per 3sec TR in an interleaved fashion.

A labmate told me that for most Siemens sequences, if there are an even number of slices per TR, then an even slice is collected first, and hence the slice order sequence would be: 2 4 6 8 … 42 1 3 5 7 … 41. However, at least in FSL, when one chooses the default “interleaved” option for slice-timing correction, it assumes that an odd slice is collected first.

How do I account for this interleaved, starting-with-even-slices ordering in AFNI? Do I set -tpattern to alt+z2 in my to3d command? Or should I pass in a customized @filename of some sort?

Thanks in advance!
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Subject Author Posted

need help with slice timing correction

lisam October 09, 2014 12:34PM

Re: need help with slice timing correction

rick reynolds October 09, 2014 01:15PM

Re: need help with slice timing correction

lisam October 09, 2014 01:37PM