fMRIprep dummy scans more than needed

[ilaria]

Hello,

I’ve run fMRIprep indicating 6 dummy scans. I found out later that 5 were acquired before the trigger was sent.
Looking at the automatic detection in the output for all the runs, the number varies from 0 to 5 with a median and mode of 1 dummy volume detected.
Distribution of detected dummy scans:
0 volumes in 9 runs
2 in 20 runs
3 in 6 runs
4 in 2 runs
5 in 1 run

My question is:
a) should I repreprocess everything with a smaller number of dummy scans, maybe 1?
b) if not, is it OK to remove fewer scans (maybe 2 or 3) in the rest of preprocessing done with AFNI (that is to run AFNI_proc.py with tcat, blur, mask, scale and regress)?
Note: I’d like to keep the number of scans removed consistent to implement stim timing calculation similarly for all tasks/participants.

Thank you,
Ilaria

[Steven]

Hello,

@ilaria

Note: I’d like to keep the number of scans removed consistent to implement stim timing calculation similarly for all tasks/participants.

Maybe I am misunderstanding the problem, but you could just explicitly add X one-hot encoded vectors in the confounds file that will remove the first X volumes.

@ilaria

a) should I repreprocess everything with a smaller number of dummy scans, maybe 1?

No need to reprocess anything, the difference would just be in the confounds file as far as I know.

@ilaria

b) if not, is it OK to remove fewer scans (maybe 2 or 3) in the rest of preprocessing done with AFNI (that is to run AFNI_proc.py with tcat, blur, mask, scale and regress)?

I have not used AFNI_proc, but this sounds like a concern that is more specific to your task and acquisition, and not with the processing pipeline.

Best,
Steven

[ilaria]

Thanks, I think I get it.
Appreciate your time replying!
Ilaria