Doubt regarding Motion Correction in resting state fMRI

[psadil]

I can’t help with your doubt. But, regarding

@varunk

And most importantly, after I have aligned the brain volumes using, let’s say, fsl’s MCFLIRT, why do I need to regress out the motion parameters again?

you can check out this answer to a similar question:

Confounds from fmriprep: which one would you use for GLM?

To add to Chris’ reply: If yes, do we still have to use the 6 motion parameters (because this nifti file is already motion corrected using FSL and ANTs) ? The short answer is: Yes. Those parameters are for denoising, not for performing motion correction. Motion correction aligns the EPI volumes so that the same voxel refers to the same location in the brain across all volumes, and those parameters are the output of that process. However, there may be noise components that correlate with mot…

A tool like MCFLIRT focuses on aligning each of the images so that each voxel’s index refers to the same part of the brain. But, the article linked in that reply (Friston, et al. 1996) details that another part of the issue with motion is a voxel’s history of excitement by the RF pulses. Without motion, the nuclei excited within a given voxel will have a chance to relax back to some consistent value. With motion, a voxel might become re-excited before completely relaxing, so the signal it gives will be dependent in some unwanted way on its history (i.e., in a way that doesn’t really depend on cognition/neurophysiology). That extra dependence can be mitigated by including the estimated movement parameters in the GLM as regressors.