Is it possible to calculate local Echo time maps with AFNI?

Hello afni experts,

I came across a research paper, which showed that the effective echo time in a scan can vary in different regions of the brain due to local variations of magnetic susceptibilities causing spatial variations in BOLD sensitivity.
"The impact of Echo Time Shifts and Temporal Signal fluctuations on BOLD Sensitivity in presurgical planning at 7 T, Investigative Radiology 2019 "
They also showed that sometimes TSNR was high but the BOLD sensitivity was low because the local Echo time was strongly reduced. Therefore, they recommend to consider both, local variations in Echo Time and TSNR (for example as product metric) when trying to evaluate BOLD sensitivity.

  1. I am just wondering if anybody has an opinion on that? I can not find many other research papers on that topic but based on this work, it would make a lot of sense to me to consider local Echo Time maps in addition to TSNR maps as QC .

  2. My second question is not directly related to AFNI but rather to the sequence. They describe that for the calculation of a local TE map, multi echo GE scans need to be acquired.They used as TE 5, 10 and 16 ms. They use these scans to calculate a GE field maps from which they then derived local TE. Does anyone happen to know if the TE choice of 5, 10 and 16 is random or if it has to follow some kind of logic? I am not sure what Te to chose if we would want to collect these scans.

  3. My third question is then of course is there a way to calculate local TE maps based on these scans with afni? I have not found any afni function for that purpose.

Thank you very much in advance!

just wanted to follow up on this in case it was forgotten.


Hi Carolin,

I do not have a strong understanding of this, but note that with ME data, the @compute_OC_weights program calculates voxelwise T2* estimates. Maybe that is along the lines of what you are looking for.

See the -help output for details.

  • rick

Hi, Carolin-

As a follow-up to this query, I've been in touch with some of the authors of this paper you pointed to:

  • Dymerska B, De Lima Cardoso P, Bachrata B, Fischmeister F, Matt E, Beisteiner R, Trattnig S, Robinson SD. The Impact of Echo Time Shifts and Temporal Signal Fluctuations on BOLD Sensitivity in Presurgical Planning at 7 T. Invest Radiol. 2019 Jun;54(6):340-348.

... and they have kindly made code publicly available (using Matlab) for this calculation, with some additional updates to be able to handle partial Fourier acquisitions and to calculate the correct minimal TE allowed. The link for that is here on GitHub.

The authors said they were also happy to receive any feedback via email or as a GitHub Issue.


Hello Rick and Paul,

Thank you very much for your replies! Thank you so much for letting me know that they made the code available on GitHub! I did previously message the corresponding author but have not heard back. I am glad some communication is established now.

Thank you again !
Best Carolin