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 02, 2021 11:18AM
I got a reply from the author of the longitudinal pipeline!

Hi Robin,
the long-processed images are all in the same space as the base image. This is -kind of- in the middle between your two time points (e.g. if the head is tilted left in TP1 and right in TP2 it will be upright) . 

So if you want to use that mask in your fMRI analysis you need to register the fMRI with images from the base dir or one of the longitudinal time points instead of with the original T1 image . 
Best, Martin 

So yes, it all makes sense! Your fix fixed the normal recon-all. And the output ROI's in the .long dirs are in "tempalte space" and should not overlap with the orig input data! We will use either the T1.nii.gz or SurfVol from the long.TP2 directory as SSWarper input!



Edited 2 time(s). Last edit at 09/03/2021 05:35AM by Robin.
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Subject Author Posted

ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper?

Robin August 31, 2021 04:17PM

Re: ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper?

ptaylor August 31, 2021 05:48PM

Re: ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper? Attachments

Robin September 01, 2021 02:12PM

Re: ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper?

ptaylor September 01, 2021 09:03PM

Re: ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper? Attachments

Robin September 02, 2021 05:48AM

Re: ROI miss-match with orig T1 when using recon-all (and longitudinal) output in SSwarper?

Robin September 02, 2021 11:18AM