Using Control Points to Fix Intensity Normalization
To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.
Here is the image of OAS2_0121_MR1_before (slice 87) and OAS2_0121_MR2_before (slice 93). These are from the cross-sectional data.
Notice that the intensity for this area is only around 90 something instead of 110. You should put control points on these slices and all the adjacent ones. Because this problem occurs in both cross-sectionals, the base, and subsequently the longitudinals, are also affected. In cases like this, it depends on which data you are planning to use, you can choose to edit either the cross, base, or long. Control points work in all three stages. In this example, we're demonstrating what the effect will be when adding control points at the very beginning of the stream - in the cross-sectionals.
After you are satisfied with your control points placements, save it, and run the following commands.
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR1_before recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR2_before
After that is complete (or when the CA normalization step is complete - you can check in the recon-all-status.log), you can start rerunning the base.
recon-all -base OAS2_0121 -tp OAS2_0121_MR1_before* -tp OAS2_0121_MR2_before -all*
The last step is to rerun the longitudinals.
recon-all -long OAS2_0121_MR1_before* OAS2_0121 -all recon-all -long OAS2_0121_MR2_before* OAS2_0121 -all
*note: