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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Robin
September 28, 2017 10:23AM
Hi!

I convert our DICOMS to .nii via dcm2niix and when running 3dinfo -slice_timing ../../data/sub01/rest1.nii I got worried: 
3dinfo -slice_timing ../../data/sub01/rest1.nii

** AFNI converts NIFTI_datatype=4 (INT16) in file ../../data/sub01_TF/rest1.nii to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000|0.000000
To me that indicates that there is no information in the .nii file to find for the AFNI-function, right? This means that my preprocessing is just copying my data and don't preform any slice timing corrections?

When running pre-processing on this particular dataset the output of tshift is: 
3dTshift -tzero 0 -quintic -prefix pb02.rest2_sub32.r01.tshift pb01.rest2_sub32.r01.despike+orig
++ 3dTshift: AFNI version=AFNI_17.2.07 (Aug  9 2017) [64-bit]
If it is the case that AFNI does not know the order how do I tell afni_proc.py that it is ascending? Would this be correct?

-tshift_opts_ts -tpattern seq-z
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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