Marking scans as dummy scans even though I have set dummy scans to 0

#1

Hello,

I ran a participant through fmriprep yesterday (latest version) and noticed that for one of the fMRI runs the first volume was marked as a dummy scan, even though I set dummy scans to 0. I trim dummy scans prior to running fmriprep using trimstart. Below is my script if it is helpful. It was HMIST_run-02 scan that contained the dummy scan.

run: fmriprep
bidsnames:
anat:
T1_MEMPRAGE_64ch_RMS: T1w

func:
Easy_MIST: task-EMIST_run-01_bold
Hard_MIST1: task-HMIST_run-01_bold
Hard_MIST2: task-HMIST_run-02_bold
rest1: task-rest_run-01_bold
rest2: task-rest_run-02_bold
rest3: task-rest_run-03_bold
rest4: task-rest_run-04_bold

fmriprep:
freesurfer: True
aroma: True
return-all-components: True
ramsize: 16
output-spaces: MNI152NLin6Asym:res-2 anat fsaverage
dummy-scans: 0
preprocess:
trimstart:
task-EMIST_run-01_bold: 0
task-HMIST_run-01_bold: 0
task-HMIST_run-02_bold: 0
task-rest_run-01_bold: 8
task-rest_run-02_bold: 8
task-rest_run-03_bold: 8
task-rest_run-04_bold: 8

fmriprep-version: 23.0.2

#2

Let me jump in here and clarify. The actual command Emily is running (after my fmriprep wrapper gets done processing that configuration file) is:

    /cm/shared/singularity/images/fmriprep-23.0-latest.simg \
    /data/belleau_lab/TeenStress/Test/E7878404 \
    /data/belleau_lab/TeenStress/Test/E7878404/derivatives \
    participant \
    --fs-license-file /cm/shared/freesurfer-license.txt \
    --participant_label TS002 \
    --output-spaces MNI152NLin6Asym:res-2 anat fsaverage \
    --n_cpus 4 \
    --mem-mb 16384 \
    --notrack \
    --use-aroma \
    --use-syn-sdc \
    --return-all-components \
    -vv \
    -w  /data/fmriprep-workdir/ebelleau

Note that no --dummy-scans flag is passed to fmriprep.

#3

Hi @dmd and @ebelleau,

I do not know the mechanisms of your custom wrapper, but if you add --dummy-scans 0 to the final fmriprep command, then no dummy scans should be produced.

Best,
Steven

#4

Hi,
This turns out to be my fault, yep. I thought the default for --dummy-scans was 0, but it’s not - the default is automatic detection.