the last couple of days I encountered some issues with my preprocessing pipeline.
After successful preprocessing, I wanted to use the estimated head motion regressors as covariates for DCM and RS analyses. While working with the output data, I noticed that my input data had a different orientation than the output images (LPS → RAS). Then I wondered at what point the head motion estimation was performed, and it seems that it is happening with the original orientation and not after a reorientation step (is reorientation of EPIs implemented or is it only performed during registration from EPI to T1w?).
Therefore, I preprocessed my data once in the original orientation (LPS - ‘fmriprep_unreorient’) and after reorientation to the initial space (RAS - ‘fmriprep_reorient’) and plotted the calculated motion regressors:
They are actually inverted for the x and y coordinates due to the different original orientation.
I think it might be a problem to use the motion regressors if the input image does not match the output orientation, or do I have a misunderstanding? It might be useful to align the EPIs to the template/output orientation before mcflirt calculates the head motion regressors.
Thank you in advance for your valuable comments on this topic!