[Freesurfer] Editing pial surface and aseg

2017-06-30 Thread Lya Katarina Paas Oliveros 
Dear FreeSurfer team

I am correcting some structural MRI scans after the automated surface-based 
analysis and the automated segmentation.

I would like to know if you have any information about how often the Voxel Edit 
is used and if it makes sense to correct the subcortical segmentation. I have 
identified specifically problems with the shape of the putamen and its borders, 
in some cases the shape of the putamen overlaps with the cortex.

Additionally, if I am editing both the Pial and WM surfaces with "Recon Edit" 
and the subcortical segmentation with "Voxel Edit", after saving both changes 
can I run both analysis at the same time (recon-all -autorecon-pial -subjid AND 
recon-all -autorecon2-noaseg -autorecon3 -subjid)? Or do I need first to do, 
for example, Recon Edit, save the changes and run the analysis and then do 
Voxel Edit, save the changes and run the other analysis?

1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Ubuntu 16.04 LTS

Thank you very much in advance.

Best regards,
Lya Paas
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[Freesurfer] surface inaccuracies around the optic chiasm

2017-06-30 Thread Gabor Perlaki 
Dear all,


I use Freesurfer 6. In some of my subjects the surfaces (both pial and
white) intruding into the optic chiasm. However, when I check the
aparc.DKTatlas+aseg.mgz it seems that although the surfaces are wrong, the
region is segmented as optic chiasm. Can I ignore this type of surface
inaccuracies similarly to surface inacurracies around the amygdala and
hippocampus?

Best Regards,
Gabor
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but does not contain patient information, please contact the sender and properly
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