Hi Bruce,

Exactly I want to be sure that I process my data in the same way, so not introduce bias with partially use of -bigventricles option.

1) I tried the recon-all process on AD patient with big ventricles and atrophy with and without the -bigventricles option. I am not pretty sure of which process is the best in terms of segmentation according the aseg.mgz ? (I'll send you T1 and aseg.mgz for the two process)
2) Considering cortical atrophy, a lot of gray matter hasn't been taken account in the cortex segmentation. Is there an automatic way to improve the cortical segmentation in case of visible atrophy ?

Best regards,
Matthieu

2015-12-03 18:03 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
Hi Matthie

do you find that it doesn't work well without bigventricles? You just
want to be sure that you process your data in the same way so there is no
bias in the results. We have found that most early AD cases work fine
without needing special flags. It's more for late stage AD or hydrocephalus
and such.

cheers
Bruce



On Thu, 3 Dec 2015, Matthieu
Vanhoutte wrote:

> Dear FreeSurfer experts,
>
> My question is in the title. I'm working on Alzheimer case where most of the cases have large
> ventricles. Is it better in general use to apply -bigventricles option on all subjects (for
> homogeneous calculus or something like that...) or to distinct subtle cases of patients with not so
> big ventricles ?
>
> Thanks in advance for helping !
>
> Best regards,
>
> Matthie
>
>
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