I think it should be ok. It will be a bit slower, but shouldn't reduce accuracy I don't think. Try it and see
Bruce
On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:


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Hi Bruce,

Thanks, but in this case will recon-all with -bigventricles flag work well on 
normal patients
without big ventricles ?

Best,
Matthieu

2018-09-18 15:56 GMT+00:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
      Hi Matthieu

      yes, you will want to run all of your subjects with it

      cheers
      Bruce
      On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:


                    External Email - Use Caution        

            Dear Bram,

            It looks like the -bigventricles flag fixed my problem with my 
specific
            subject. Not only, this took
            into account large ventricles but also corrected grey matter 
segmentation
            from extra Dura tissue
            that was erroneously segmented in GM.

            I understand the first point of amelioration allowed by the flag 
but don't
            understand where the
            second point come from ?

            If I used the -bigventricles flag for all my atrophied and large 
ventricles
            patients and not for my
            healthy patients, wouldn't it introduce a bias when further 
statistically
            comparing groups between
            them ?

            Best,
            Matthieu

            2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder 
<brdiam...@mgh.harvard.edu>:
                  If you haven't already, you may want to run the subject 
through
            recon-all with the
                  -bigventricles flag since it looks like the lateral ventricle 
was
            significantly
                  mislabeled in the aseg. If using the -bigventricles flag 
doesn't fix
            your problem, you
                  can edit the aseg.mgz manually by following the directions in 
this
            tutorial. Then run
                  the following command (again, substituting <subj_id> for your
            subject's id):
            recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

            I would try this before doing the wm.mgz edits I suggested in my 
previous
            email.

            Best,
            Bram

___________________________________________________________________________________________________
            _
            From: freesurfer-boun...@nmr.mgh.harvard.edu
            <freesurfer-boun...@nmr.mgh.harvard.edu> on
            behalf of Diamond, Bram Ryder <brdiam...@mgh.harvard.edu>
            Sent: Friday, September 14, 2018 11:07:42 AM
            To: matthieuvanhou...@gmail.com
            Cc: freesurfer@nmr.mgh.harvard.edu; astev...@nmr.mgh.harvard.edu
            Subject: [Freesurfer] Troubles to determine the type of recon 
editing needed
             

            Hi Matthieu,


            I've taken a look through the files you shared with us and I see 
the poor
            surfaces in the
            posterior right hemisphere you were referring to in your message. 
It looks
            like your subject
            has a combination of abnormally large ventricles and significant wm
            abnormalities, so I'm
            surprised FreeSurfer did as well as it did.


            As for the recon editing - I would recommend editing the wm.mgz to 
more
            accurately represent
            the wm from slice 84 to 39. You can take a look at the white matter 
edits
            tutorial for details
            on how to do that. Then run the following command (substituting 
<subj_id>
            for your
            subject's id):


            recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>


            The surface reconstruction may also benefit from labeling the right 
lateral
            ventricle in the
            wm.mgz (as an intensity of 250) - but I'm not certain since you 
didn't send
            us the surfaces
            for the left hemisphere. Before you do that, edit the wm.mgz as 
explained in
            the tutorial and
            tell us how that goes.


            All the best,

            Bram


            Bram R. Diamond, BSc
            Research Technician II
            Laboratory for Computational Neuroimaging
            Martinos Center for Biomedical Imaging
            Massachusetts General Hospital
            149 13th Street 
            Charlestown, MA 02129
            (p): 617-726-6598

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