@Steven After further reflection, I think the masks belong in the dwi not anat derivatives folder as they are drawn on diffusion images, so if you agree with this, I will label this as solved:
derivatives/
lesion_masks/
sub-M2001/
dwi/
sub-M2001_space-TRACE_desc-AcuteLesion_mask.nii
sub-M2001_space-TRACE_desc-ChronicLesion_mask.nii
sub-M2001_space-TRACE_desc-lesion_mask.nii
sub-M2001/
anat/
sub-M2001_T1w.nii
dwi/
sub-M2001_rec-TRACE_dwi.nii
sub-M2001_rec-ADC_dwi.nii