Dear FreeSurfer Experts

 

I am using FreeSurfer on my anatomical data to use segmentations and parcellations in my fMRI analyses in AFNI. After reviewing the output from recon-all -all (FreeSurfer version 6.0.0), I noticed that one subject is missing some occipital areas in the output (e.g. aparc+aseg.mgz). Please see attached for a screenshot of the output from

 

       freeview -v mri/brainmask.mgz \

       mri/wm.mgz:colormap=heat:opacity=0.4 \

       -f surf/lh.white:edgecolor=yellow \

       surf/lh.pial:edgecolor=red \

       surf/rh.white:edgecolor=yellow \

       surf/rh.pial:edgecolor=red \

       surf/rh.inflated:visible=0 \

       surf/lh.inflated:visible=0

 

From what I read in the information on troubleshooting the output, I understand that manual editing is necessary to fix this – is this correct? I have verified that the missing areas are included in the brainmask as well as aseg.presurf. I am not sure though how to determine whether I am dealing with a segmentation error or a normalization error or maybe even a combination of both.

 

If you could give me some pointers on which steps to take, that would be highly appreciated.

 

Many thanks in advance for your help.

 

Best regards,

 

Stef