Hi Rito,

I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel value less than 110)." from https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview

Could it be that those control points grasp voxels that already have an intensity of at least 110? 

Best wishes,

Barbara

Hi All,

We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid <subject>

but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack

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