Hello,

The initial command to recon-all:

recon-all -i $FREESURFER_HOME/subjects/PPG1156/1156MPRage.nii.gz -autorecon1 -autorecon2 -subjid MGZ

exited with errors during SubCort Seg. At this point, I am attempting to obtain subcortical segmentation only (aseg.mgz, wm.mgz, aseg.stats), but would like to eventually run entire recon. I have attached the recon-all.log.

I checked the tal transform and skullstrip- both looked OK. The scan is of a subject with Huntington's Disease so the ventricles are a bit enlarged and there is significant asymmetrical atrophy such that at least one area of brainmask.mgz was labeled as 57 (Right-Lesion). Also, there seems to be intensity variations (artifact?) A-P across cortex on slices around mid-line in sagittal view.

Any ideas? Please let me know if you'd like me to upload any/all files.

Thank you for your help,

Julie

Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676