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