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Using Control Points to Fix Intensity Normalization

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 (it is best to remove the existing longitudinal directories).

recon-all -long OAS2_0121_MR1_before* OAS2_0121 -all
recon-all -long OAS2_0121_MR2_before* OAS2_0121 -all

*note: Here we use OAS2_0121_MR1_before and OAS2_0121_MR2_before as the cross ids to keep it consistent with the files you are using for the edits, but note that in your actual data, when rerunning the base or the longitudinals, the ids cannot be renamed to something else (e.g. _before, _edit) unless it's after it's already ran/reran. So if you want a copy of the before version, rename that to tpid_before and edit the tpid version.