Dear all,

In three of my subjects one of the sides of the T1 scan is brighter than the other side (probably a coil problem). This resulted in the recon-all processing stream identifying not enough white and gray matter, even though the brainmask.mgz included the whole brain. Since I will use my T1 scans as registration for my DTI scans only the white matter is of importance and loss of gray matter is not really an issue.

I manually edited the wm.mgz using the voxel edit function. I tried to rerun the pipeline in the same subject folder with this command: recon-all -autorecon2-wm -autorecon3 -s 0008_smri_t1 with the wm.mgz being replaced by my edited version (red overlay in attached screenshot). It finished without errors according to the log files (one is attached), but no changes were made to the output files (e.g. aparc+aseg and lh.white) as can been seen in the screenshots.

Do you have any idea why the white matter that I added in wm.mgz has not been included in the new output files? Secondly, do you have any idea how I could fix this?

I am still a bit new to Freesurfer, so help would be very welcome!

Kind regards,

Jari Gool Department of Neurology - Leiden University Medical Center - The Netherlands