Fmriprep doesn't seem to be able to automatically produce some results in the func folder

[Yunhong_Wang]

Hello all,

I checked my func output compared to standard fmriprep output, and found that my fun lacked some outputs related to T1w and aseg.

The figure of standard output is from fmriprep documentation:

This is my code:

singularity run \
        --cleanenv \
        -B $BIDS_DIR:/data:ro \
        -B $DERIVS_DIR:/output \
        -B $WORK_DIR:/work \
        -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME}:ro \
        -B ${SINGULARITYENV_FS_LICENSE}:/freesurfer_license:ro \
    ${FMRIPREP} /data /output \
    participant --participant_label $subject \
    -w /work \
    -vv \
    --fs-license-file /freesurfer_license \
     --fs-subjects-dir /output/freesurfer \
    --mem-mb 64000 \
    --n-cpus 16 \
    --write-graph \
    --output-spaces MNI152NLin2009cAsym:res-2 \
    --return-all-components

If I want to accquire the T1w and aseg related outputs, do I need add T1w and fsnative space to --output-spaces like this:

--output-spaces T1w fsnative MNI152NLin2009cAsym:res-2 \

Best,
Yunhong

[effigies]

No (aparc+)aesg output from fmriprep

Summary of what happened: Preface: I am new to fMRIPrep. End goal: Extract timeseries from various ROIs. Overview: I have run fMRIPrep and there are no errors mentioned in the .html files for each subject. Based on some reading by others on this site and additional information around the internet, it seems like I should be using the (aparc+)aseg files generated by fMRIPrep to created a mask for my data. However, there are no such files in my derivatives directory. I do have /bids/derivatives/…

[Yunhong_Wang]

Thank you for your help @effigies

I have a question that why T1w and aseg file don’t generate automatically?

I am testing to add the T1w and fsnative to --output-spaces and rerunning the fmriprep using the same output directory. Work is going, and some outputs generate:

But I’m not sure this is the right approach, what do you think?

Best,
Yunhong