Fmriprep on multi-echo data: Exporting individual echos in MNI space

Software Support
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1

Summary of what happened:

I am currently working with multi-echo data (3 echos) and would like to have the preprocessed timeseries for each individual echo in MNI space (MNI152NLin2009cAsym). I used the fmriprep flag –me-output-echos, but this only exports the echo timeseries in the native space it seems. Is it possible to export them in MNI space as well? If not, is there an alternative way to transform the native-space echos to MNI space after fmriprep was run?

Thanks in advance,
Philipp

Command used (and if a helper script was used, a link to the helper script or the command generated):

–me-output-echos

Version:

23.1.3

Environment (Docker, Singularity, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

BIDS

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

2

You can use antsApplyTransforms to transform the echos to MNI. What is the use case for having individual echos in MNI space?

3

Cool, thank you, I’ll try that. The use case here is we intend to calculate contrast-to-noise ratio (CNR) of the multi-echo data, taking into account the signal contributed by each individual echo. Our MRI physicist thinks it would be best to calculate CNR = tSNR * effective TE, where effective TE = TE * its weight in multi-echo combination * its signal (calculated for each echo and divided by the sum).