Hi there,
I am using freesurfer v5.3.0 to recon some 7T structural scans.
I have been adding some control points to compensate for poor temporal lobe contrast, something that has worked just fine many times before. However, now when rerunning the recon process as follows:
recon-all -autorecon2-cp -autorecon3 -subjid <name>
It looks like the reprocessing has not taken the control points into account at all, and actually has changed the segmentation in areas that were previously fine. My control.dat file is in the subjid/tmp folder
and is populated correctly so I assume it should be able to be located.
Can anyone offer any advice on what might be going on? The same error is also being experienced by a colleague here.
Thanks a lot!
Sarah Finnegan
Nuffield Department of Clinical Neurosciences
University of Oxford, John Radcliffe Hospital
Oxford, OX3 9DU