Hi experts,

We want to combine two large datasets (of patients with different diseases) that have been processed and manually edited using Freesurfer 5.3 and Freesurfer 6.0.

From the Freesurfer website and previous posts, we have read that we should re-run the Freesurfer 5.3 data that has been manually edited (both brain masks and pial surfaces) through Freesurfer 6.0 using recon-all and using the -continued flag, and that the manual edits from 5.3 should carry over.

However, we have found that around one-third of subjects have skull stripping errors after rerunning through 6.0. Has anyone else found this? Have we missed something?

A related question: We have heard it argued that if the data has been manually edited and quality checked, the version of Freesurfer which it is run through should not matter, therefore it is ok to combine data from different versions – what do you think of this argument?

An additional argument along those lines that we have heard is: If one were to re-process data with a later version of Freesurfer, using edits from an older version would introduce biases from that version – what are your thoughts on this argument? 

Thank you.

 

Lisanne