Fmriprep not combining multi-echo in output

Software Support
,
1

Summary of what happened:

I have multi-echo fmri data and when i use fmriprep to process them, i don’t feel the output has the echos combined. in my summary report, i do see a T2* plot but when i check output files and keyword search for tedana in the log file, i couldn’t find any pipeline set up for tenada. i thought fmriprep is suppose to automatically combine the echos, am i missing some flag that i should set?
in my output of fmriprep, should i assume sub-01_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz is already multi-echo combined? i am not sure and i thought these echos are not combined since in the html file, i didn’t see a description of combing echos:

image
image1920×790 268 KB

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

singularity run \
    --bind /dsxxxxx-download:/data \
    --bind /dsxxxxx_out:/out \
    fmriprep-23.2.3.simg \
    /data /out participant \
    --participant-label "01" \
    --fs-no-reconall \
    --use-syn-sdc warn \
    --nprocs 8 \
    --omp-nthreads 8

Version:

I am using singularity version of fmriprep 23.2.3

Environment (Docker, Singularity / Apptainer, custom installation):

i use singularity version of fmriprep

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

my data is in bids format

bids-validator@1.14.6
e[32mThis dataset appears to be BIDS compatible.e[39m
        e[34me[4mSummary:e[24me[39m                    e[34me[4mAvailable Tasks:e[24me[39m        e[34me[4mAvailable Modalities:e[39me[24m 
        5649 Files, 103.37GB        rest                    MRI                   
        301 - Subjects                                                            
        1 - Session                                                               


e[36m	If you have any questions, please post on https://neurostars.org/tags/bids.e[39m
250716-15:19:35,175 nipype.workflow IMPORTANT:
	 Running fMRIPrep version 23.2.3

         License NOTICE ##################################################
         fMRIPrep 23.2.3
         Copyright 2023 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250716-15:21:05,664 nipype.workflow IMPORTANT:

Screenshots / relevant information:

when i search for tedana in log, i didn’t get any match.

image
image1474×1248 156 KB

the func folder of fmriprep output looks like:
image
image1180×1598 247 KB

2

The desc-preproc_bold files are the optimally combined data.

3

Hi @tsalo thank you for the swift reply!
I wonder why do i not see a tedana pipeline set up in the log file of the process? i checked tedana’s documentation and i was expecting files like registry.json or desc-tedana_registry.json from tedana. I thought version 23.2.3 of fmriprep use tedana to do multiecho combination?

4

fMRIPrep doesn’t run the full tedana workflow- it just runs t2smap to estimate T2*/S0 and combine the data across echoes.

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