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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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possible to skip motion realignment? #2594

Open GerardYu opened 2 years ago

GerardYu commented 2 years ago

hi i'm using the CAM-CAN dataset preproc_fMRI_realignunwarp volumes (fMRI volumes realigned and unwarped from Fieldmaps). Since these volumes are already motion realigned, I wonder if its possible to skip the motion realignment in the fmriprep preprocessing pipeline? or is it ok run the full fmriprep preprocessing pipeline on these 'slightly' preprocessed volumes?

effigies commented 2 years ago

We don't have the ability to skip HMC altogether, at present. Thanks to the single-shot resampling, I don't think you should face any penalty in terms of accumulated numerical error for very small motion parameters. The main downside will be the time of recomputing the parameters and verifying that large motion is not detected.

effigies commented 2 years ago

Just to be explicit: I think it should probably be okay, as long as you use --ignore fieldmaps slicetiming. Worth trying and reporting back.