Removing Dummy Scans - fMRIPrep

Software Support
1

Summary of what happened:

Hi, I am new to using fMRIprep and I have a query about Dummy Scans.

If possible, I would ideally like to remove the dummy scans (i have 5) before running fMRIprep so that it closely matches how I would’ve preprocessed my data in SPM. However, I cannot see experience of people doing this. I have raw dicom files, that I am converting to .nii and putting into BIDS via Heudiconv and then running fMRIprep. Is there a way to correctly remove dummy scans (as you would in SPM), do you need to do this prior to using Heudiconv, or would this cause inconsistencies in the headers and json files? Does anyone have experience here?

Alternatively, I can see if that I could put --dummy-scans 5. However, it is not clear as to what this does.
Firstly, how are those 5 dummy scans then treated in the fmriprep processing steps? Secondly, in my first level analysis script in SPM, I adjust my task times to take into account that I have deleted the first 5 volumes - would i still do this, because it seems that using the tag doesn’t actually remove the dummy scans.

2

Hi @MRI_New,

It adds one-hot encoded regressors to the confounds files that can be imported into first level model denoising.

You would not adjust the event timings.

Best,
Steven

3

Hi, Thank you for getting back to me so fast. Does this mean that it is not feasible to simply remove the volumes before running fMRIprep?

4

Hi @MRI_New,

You can do that, but it is typically recommended to not mess with raw data.

Best,
Steven