MP2RAGE

MP2RAGE is the anatomical MR acquisition used for BST3 7T Projects: 7T Anatomical Acquisitions and SPA MR. Processing has included running UNICORT before providing the images to freesurfer (MTR SNR, Hc Myelin), see Freesurfer for BrainMechR01 (7T).

From the 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 (Marques et al. 2010).
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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 ''MP2RAGE'' specific notes in the qMRI appendix for further information.

As of 2025-05-16, fmriprep does not handle mp2rage natively and faking a _UNIT1.nii.gz as _T1w.nii.gz leads to bad skull stripping. Instead we run 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 neurostars discussion.