Fig. 2.

illustrates the overall T1w/T2w transmit field correction pipeline operations and outputs, with inputs and outputs represented by horizontal boxes and processing steps by vertical boxes. Options (depending on specifics of data acquisition) are indicated with different colors (purple for real transmit field, green if Siemens PreScan Normalize (PSN) was used on all images, and blue if motion compensation for the receive field is needed because PSN was not used). Lines that intersect a step (without an arrowhead/passing under the step) skip that particular step. The simplest form of the pipeline (green path) would require that the T1w and T2w images (and GRE/SE images if the pseudo-transmit approach is used) have undergone PSN or the equivalent from another vendor, which permits skipping the Receive Field Correction with Motion Compensation step (blue paths). Bold text indicates the primary outputs of interest for downstream analyses. In all cases, outputs are in CIFTI, NIFTI physical volume, and NIFTI MNI volume spaces.