Hello,
I have some basic questions with regards to adding control points to fix the WM intensity normalization. I am running some subjects through autorecon 1 and 2 only (we are not concerned with subcortical structures). The reconstructed volumes had a lot of missing grey matter in the lateral temporal lobe, and my intention is to fix this by adding WM control points (the intensity is also off for WM in places). Long story short, I have the control points added and saved, and then I run the subjects through recon-all autorecon2-cp.
1) Am I correct that autorecon3 will not be necessary if I am only including cortical structures? (I see it is included in the command line on the control point tutorial.)
2) Once I run the subjects through autorecon2-cp, when I open them in tkmedit the segmentation still has not changed - the control points are still there as before. Do I need to run the subjects through some other processing step before I will see the changes? (I am doing tkmdedit SUBJECT brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white)
3) Based on the workflow in http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction, it seems that control points need to be added directly after autorecon1. I am actually adding the CPs on subjects that have gone through autorecon2 already. Is this a problem or is it still possibe? (If a problem I can reprocess the data.)
Sorry if these are painfully obvious questions, but I seem to be slightly confused with the processing pipeline.
Much thanks,
John Sheppard