Hi Sarah

if you upload the subject we will take a look. The best would be if you have upload the entire subject dir twice - once before and once after adding the additional control points Bruce

On Wed, 9 Nov 2016, Sarah Finnegan wrote:

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 Email: sarah.finnegan@stcatz.ox.ac.uk