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

History of AFNI updates  

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November 20, 2020 03:53PM
Hello,

While I have not gone through the entire script so well yet, it jumped out that you originally aligning each run to volume index 0 for that run. The MIN_OUTLIER volume is generally a much better base volume, as it is expected to have very little motion artifact. Consider this set of options (part of Example 13):

-align_opts_aea -cost lpc+ZZ -giant_move                \
                 -volreg_align_to MIN_OUTLIER                            \
                 -volreg_post_vr_allin yes                               \
                 -volreg_pvra_base_index MIN_OUTLIER                     \
                 -volreg_warp_final_interp wsinc5                        \

I hope that works a little better, though for noisy data, I could see averaging being better.

But you have index 86 above. What does that index imply?

- rick
Subject Author Posted

difficulties with run to run alignment, possible solution

dowdlelt November 20, 2020 01:59PM

Re: difficulties with run to run alignment, possible solution

ptaylor November 20, 2020 03:49PM

Re: difficulties with run to run alignment, possible solution

dowdlelt November 20, 2020 04:32PM

Re: difficulties with run to run alignment, possible solution

ptaylor November 20, 2020 05:00PM

Re: difficulties with run to run alignment, possible solution

dowdlelt November 20, 2020 05:13PM

Re: difficulties with run to run alignment, possible solution

rick reynolds November 20, 2020 03:53PM

Re: difficulties with run to run alignment, possible solution

dowdlelt November 20, 2020 04:57PM

Re: difficulties with run to run alignment, possible solution

dowdlelt November 22, 2020 06:24PM