Fmriprep: flair images

Summary of what happened:

I am using fMRIPrep 22.1.1 on Ubuntu 20.04 LTS with docker. My input includes both T1w images and T2 FLAIR images. The T2 shows up in the “mri/orig” folder of freesurfer and this shows up in the log file:
resume recon-all : recon-all -parallel -subjid sub-ID -sd /out/sourcedata/freesurfer -FLAIRpial -cortribbon

However, the fMRIPrep output does not mention T2 FLAIR at all. Therefore, I am unsure if the T2 FLAIR were taken into account by freesurfer. The FLAIR images have a resolution of 1x1x1mm. Could it be that freesurfer has used the T2 FLAIR, but it is not mentioned in the fMRIPrep output?

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

I created the BIDS version with dcm2bids with these specifications:

  "dataType": "anat",
        "modalityLabel": "FLAIR", 
        "criteria": {
            "SidecarFilename": "020*"
        "dataType": "anat",
        "modalityLabel": "T1w", 
        "criteria": {
            "SeriesDescription": "T1w_MPR", 
            "SidecarFilename": "007*"

And this is the fMRIPrep command I used:

fmriprep-docker ~/Desktop/ISP/EMOPRED/BIDS_data ~/Desktop/ISP/EMOPRED/fMRIPrep_data participant --participant-label ID --fs-license-file ~/Desktop/Afton/FreeSurfer/license.txt --skip-bids-validation --n-cpus 12 --use-aroma --output-spaces MNI152NLin6Asym


fMRIPrep 22.1.1

Environment (Docker, Singularity, custom installation):

Docker on Ubuntu 22.04 LTS

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


Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

If -FLAIRpial showed up in the recon-all command and it didn’t crash, you’re fine.

I’ll make an issue to ensure we add this to the boilerplate text.

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