External Email - Use Caution
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:
>
> External Email - Use Caution
>
> 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 <fischl@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 <BRDIAMOND@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-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on
> behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>
> Sent: Friday, September 14, 2018 11:07:42 AM
> To: matthieuvanhoutte@gmail.com
> Cc: freesurfer@nmr.mgh.harvard.edu; astevens@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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