====== MP2RAGE ======

''MP2RAGE'' is the anatomical MR acquisition used for BST3 7T Projects: [[:grants:7t:mr:anat]] and [[:grants:spa:mr]]. Processing has included running [[:tools:UNICORT]] before providing the images to [[:tools:freesurfer]] ([[:projects:mtrsnr|MTR SNR]], [[:projects:hpcmyelin|Hc Myelin]]), see [[grants:7t:mr:freesurfer]].

From the [[https://bids-specification.readthedocs.io/en/stable/glossary.html#objects.suffixes.MP2RAGE|BIDS description]]
> The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([[https://linkinghub.elsevier.com/retrieve/pii/S1053811909010738|Marques et al. 2010]]).
> ...
> Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from ''T1w''. Please see [[https://bids-specification.readthedocs.io/en/stable/appendices/qmri.html#unit1-images|''MP2RAGE'' specific notes]] in the qMRI appendix for further information.

As of 2025-05-16, [[:tools:fmriprep]] does not handle mp2rage natively and faking a ''_UNIT1.nii.gz'' as ''_T1w.nii.gz'' leads to bad skull stripping. Instead we run [[:tools:freesurfer]] on the mp2rage first and use the skull stripped output as input to fmriprep with the ''%%--skull-strip-t1w skip%%'' option. Also see this [[https://neurostars.org/t/mp2rage-in-bids-and-fmriprep/2008/24|neurostars discussion]].