Wrong T2* map estimation of multi-echo data

Dear tedana Expert,

I am writing to seek your assistance regarding an issue I encountered while using tedana to generate T2* maps. After merging my data with tedana, the resulting T2* map appears to be problematic. Specifically, the values on the horizontal axis of the histogram seem incorrect. Additionally, when I open the T2star.nii file, the image appears abnormal.

Interestingly, when I do not use tedana for merging, the output T2* map is correct. Given this discrepancy, I am uncertain about the root cause of the issue and would greatly appreciate your guidance on how to resolve it.

Thank you very much for your time and assistance.

Best regards,
Ge Qiu

That is odd indeed. Can you share the command you used for tedana? I’m assuming you used it from the terminal.

@G_Q is there any chance you ran tedana with echo times in seconds instead of milliseconds?

I just realized this morning that my echo times were being entered in seconds. The Auto_tedana script that is recommended for use after fmriprep pulls the echo times from the bids json which are stored in seconds not milliseconds (at least for mine from a Siemens Prisma). I added this line to Auto_tedana.py

echo_times = [i * 1000 for i in echo_times]

to convert the echo times to milliseconds. Having the echo times in seconds didn’t seem to change anything except the x-axis units for the T2* histogram.

1 Like