Surface reconstruction problem with fmriprep

Software Support
1

Summary of what happened:

I want to use fmriprep to preprocess a fMRI dataset. I already have the Fastsurfer recon data processed using micapipe Structural processing — micapipe documentation. How could I feed these data to fmriprep so that I can skip the recon step using freesurfer in fmriprep?

Moreover, if I directly use the freesurfer in fmriprep, how long will it take for one subject?

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

Here is the code without reconall, how can I add fastsurfer output to it?

singularity run --cleanenv -B $TEMPLATEFLOW_HOME:/templateflow $HOME/software/my_images/fmriprep-latest.simg \
  $bids_root_dir $HOME/project5/preprocessing_volume/derivatives1 \
  participant \
    --participant-label 016 017 018 019 020 021 023 024 026 027 029 031 032 033 034 036 038 039 040 041 042 043 045 046 047 048 049 050 051 052 053 054 055 056 057 059 \
    --skip-bids-validation \
    --md-only-boilerplate \
    --fs-license-file $FREESURFER_HOME/license.txt \
    --dummy-scans 5 \
    --fs-no-reconall \
    --output-spaces MNI152NLin6Asym:res-2 \
    --nthreads $nthreads \
    --stop-on-first-crash \
    --mem_mb $mem_mb \
    -w $HOME/work1

Version:

24.1.0

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

Singularity

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

BIDS dataset

Relevant log outputs (up to 20 lines):

none

Screenshots / relevant information:

2

Hi @Yi_Zheng,

Do not use that flag, it disables all surface workflows.

Use --fs-no-resume and define -fs-subjects-dir accordingly.

best,
Steven

3

Thank you very much for your reply!