Dear Freesurfer list,

As I have used the QA tools on a couple recon-all jobs, I have run into an error when running recon_checker QA tools. The QA tools are not able to read many of the output files from recon-all, in the "label" directory. As I look back into the label directory, this is because many of my files after running recon have an "_exvivo" stem. For example, the QA tools cannot read the "../label/lh.BA1.label" file because in my subject directory, as it is named "../label/lh.BA1_exvivo.label". And the same is true for many other files.

After searching online for solutions to this problem I have not found any way to eliminate the _exvivio stem, but I understand that exvivo data has been used to increase the quality of images for FS v6. Is there a way to fix this when running recon-all? Or, is this problem occurring because I'm using QAtools1.2 with FS v6.0?

Best, Micah