Robust retrospective motion correction of head motion using navigator-based and markerless motion tracking techniques.

"the original data were taken from slipsager et al and available here: https://figshare com/articles/dataset/tracking_data_patient_b_/6989336 ."

"CONFLICT OF INTEREST STATEMENT Elisa Marchetto received research funding's partially from TracInnovations. Stefan Glimberg is an employee of TracInnovations."

"This research was funded in whole or in part, by the Wellcome Trust (WT200804). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. This work is also partly funded by research support from TracInnovations."

"To generate the mask corresponding to the parts of the scalp expected to move rigidly (and therefore, allowing exclusion of non‐rigid regions), we first selected the T1‐weighted (T1w) image of one dataset acquired without deliberate motion and the corresponding first FatNav volume. We registered the T1w and the FatNav volume using the FSL FMRIB's Linear Image Registration Tool function,, to have a 3D FatNav and T1w image in the same space. After applying brain extraction tool (BET),, we registered the T1w volume to the 1 mm MNI152 standard space brain., By following the same process, a 3D FatNav for each subject could be brought into a standard space, and then averaged using fslmaths from the FSLutils to obtain a standardized FatNav volume. ITK‐SNAP was used to manually define a mask in this standard space that would exclude the neck region. When estimating the motion parameters for each subject from the FatNavs, the first FatNav from the subject was co‐registered to the standardized FatNav volume, allowing the mask to be brought into subject‐space and incorporated as a weighting image to SPM's spm_realign function. Statistical difference between the image quality obtained by using FatNav‐based motion correction with and without the neck mask was assessed using the Wilcoxon signed rank test (signrank MATLAB function)."