Just want to check if you get the recon-all files that I sent for an entire subject?! 

I am also wondering if the problem with the segmentation can be related to the small size of aged Portuguese brains considering the expected size based for instance on the MNI space?! 

Because pial segmentation is including intensities under 110 and the aseg maps are also badly estimated

Em quarta-feira, 20 de fevereiro de 2019, Bruce Fischl <fischl@nmr.mgh.harvard.edu> escreveu:

hmmm, I don't see anything glairing in the log. I guess upload the subject and we'll take a look
Bruce


On Wed, 20 Feb 2019, mara alves wrote:

        External Email - Use Caution        

Here is the recon-all.log for one for old subjects.Thanks,
Mara

mara alves <mara.f.alves@gmail.com> escreveu no dia quarta, 20/02/2019 à(s) 09:57:
      Hi,
Thanks for the quick reply. What do you mean about uploading the entire subject? All the
output files of the recon -all?

Best,
Mara

Bruce Fischl <fischl@nmr.mgh.harvard.edu> escreveu no dia terça, 19/02/2019 à(s) 23:10:
      wow, that looks pretty bad. Can you send us the recon-all.log (or upload
      the entire subject and we will investigate)?
      On Tue, 19 Feb 2019, mara alves
      wrote:

      >
      >         External Email - Use Caution        
      >
      > Hi there,
      >
      > I ran the recon -all command in two samples, one of young participants and
      another of older
      > subjects.
      >
      > The segmentation worked well for young participants, however it seems that for
      older participants
      > the white.pial segmentation it is being done incorrectly. I believe it is
      segmenting the gray matter
      > instead (please see the pics attached).
      >
      > Best,
      > Mara
      >
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