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.
Notice that the intensity for the area in the bottom corner of the right hemisphere around slice 90 is only around 90 something instead of 110, and the surfaces here do not include all of the gm and wm. 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. Find all the slices that have this problem and add control points carefully on the wm voxels.
OAS2_0121_MR1 (slice 87) and OAS2_0121_MR2 (slice 93).
Once you are satisfied with your control points placements, save it, and run the following commands.
recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR1 recon-all -autorecon2 -autorecon3 -subjid OAS2_0121_MR2
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 -tp OAS2_0121_MR2 -all
The last step is to rerun the longitudinals (it is best to remove the existing longitudinal directories).
recon-all -long OAS2_0121_MR1 OAS2_0121 -all recon-all -long OAS2_0121_MR2 OAS2_0121 -all
To look at the output, open your subject in tkmedit using the following commands.
tkmedit OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs
tkmedit OAS2_0121_MR1.long.OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs tkmedit OAS2_0121_MR2.long.OAS2_0121_fixed brainmask.mgz -aux T1.mgz -surfs
Here are the output images of the base. You can see the difference in the surfaces from the before (left) and after (right) image at slice 108, although no control points were copied over. The base improved, because of the adjusted intensity values in both cross-sectionals.
As for the longitudinals, control points were automatically copied over from the cross-sectionals, and the surfaces were initialized from base, therefore making a great improvement on the surfaces for the longitudinals.
The before (left) and after (right) images from OAS2_0121_MR1.long.OAS2_0121 at slice 107.
The before (left) and after (right) images from OAS2_0121_MR2.long.OAS2_0121 at slice 108.
