Hi all,


We are processing longitudinal structural MRI data on Freesurfer 5. 0.  As our
images have some intensity problems, we were running an N3 correction
outside of FreeSurfer using a mask in order to maximize this step (as per
recommended by Boyes et al., 2008). We first ran autorecon1 and then used
the brainsmask.mgz as a mask for the N3 correction, using the following
steps.



mri_convert orig.mgz orig.mnc

mri_binarize --i brainmask.mgz --min 1 --o binmask.mgz*

mri_convert binmask.mgz binmask.mnc*

mincnorm orig.mnc orig_norm.mnc

nu_correct -mask binmask.mnc -distance 50 -iterations 1000 -stop 0.0001
-shrink 2 -fwhm .05 orig_norm.mnc nu.mnc

mri_convert nu.mnc nu.mgz*



This nu.mgz was then fed into freesurfer and autorecon1 was run over
again without
nuintensity correction. However, during this step, many of our scans are
crashing, with the T1.mgz being very dark. When the same scans were run
through Freesurfer with the nuintensitycor-3T flag (without using a mask),
there were no crashes. Do you have any advice on why the N3 correction using
the mask is crashing when re-running autorecon 1? Should we be using
different nu_correct parameters to help the process?



Thanks for your help!



Nandi
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