Dear FS Wiki
I run my scan in FS without any problem example: #@#%# recon-all-run-time-hours 8.342 recon-all -s 877 finished without error then I do some edits to the aseg in freeview edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles Once done, I re-run using recon-all -s $i -autorecon2-noaseg example: /mridata/workingdata/HIV/subjects/877 /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all -s 877 -autorecon2-noaseg in 25% of cases, I get the following error message and the process exists example: #-------------------------------------------- #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016 /mridata/workingdata/HIV/subjects/011/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz mri_normalize: aseg volume aseg.mgz must be conformed using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016 in the other no problem example: #@#%# recon-all-run-time-hours 1.116 recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016
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