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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Karelo
June 04, 2021 05:41AM
Dear AFNI experts,

I have two datasets with a different acquisition slice order (tpattern). I would like to make sure that the slice timing correction with 3dTshift is well done.

1. First dataset.
TR=2 seconds
number of slices=35
slice order= Interleaved (1,3,5,7...35; 2,4,6,8...34).
Command used: 

3dTshift  -tpattern Alt+z   -Fourier  -prefix s_001_stc.nii  s_001.nii

2. Second dataset.
TR=2 seconds
number of slices=37
slice order= Interleaved with jumps of 5 slices (1, 7, 13, 19, 25, 31, 37; 2, 8, 14, 20, 26, 32; 3, 9, 15, 21, 27, 33; 4, 10, 16, 22, 28, 34; 5, 11, 17, 23, 29, 35; 6, 12, 18, 24, 30, 36).
Command used: 

3dTshift  -tpattern Alt+z   -Fourier  -prefix s_001_stc.nii  s_001.nii

I am using the exact same tpattern for both datasets. Is this correct considering that the second dataset has different jumps between slices?
Note: The to3d program considered both datasets as Alt+z.
Thanks in advance.

Kind regards,
Karel
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Subject Author Posted

Slice timing correction in two different datasets

Karelo June 04, 2021 05:41AM

Re: Slice timing correction in two different datasets

Peter Molfese June 07, 2021 09:56AM