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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gauravm
November 18, 2012 04:04PM
Hi Dan,
Thanks a lot for the detailed response and sorry about the delayed reply, I was out of town for a few days. I managed to contact the right person at Philips after much bouncing around. He has confirmed that slice time correction is not applied during reconstruction of fMRI data. So, I need to figure out a way to make AFNI not think that the data is slice time corrected.

I just want to confirm with you the approach I tried now:
Since the proc script generated by afni_proc.py does 3dTshift as the first processing step after removing the first few TRs, there should be nothing wrong with pre-processing my data with 3dTshift before feeding it to afni_proc.py.

The best way will be to correct the header info in the nii files so that AFNI recognizes it as not-time-corrected. But I don't know how to go about doing that.

Thanks a lot, great help!
Best,
Gaurav
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Subject Author Posted

Slice timing correction issue

gauravm November 06, 2012 01:19PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 02:08PM

Re: Slice timing correction issue

gauravm November 06, 2012 03:25PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 03:38PM

Re: Slice timing correction issue

gauravm November 06, 2012 05:13PM

Re: Slice timing correction issue

Daniel Glen November 06, 2012 09:48PM

Re: Slice timing correction issue

Daniel Glen November 08, 2012 04:28PM

Re: Slice timing correction issue

gauravm November 18, 2012 04:04PM

Re: Slice timing correction issue

Peter Molfese November 18, 2012 04:33PM

Re: Slice timing correction issue

gauravm November 19, 2012 09:42AM

Re: Slice timing correction issue

rick reynolds November 19, 2012 09:55AM