External Email - Use Caution        

Dear Bram,

According recon-all help "If a subject has enlarged ventricles due to atrophy, include the -bigventricles
flag with the -autorecon2 stage in order to prevent surfaces extending into the ventricle regions. The flag directly affects the binary mri_ca_register, and mris_make_surfaces indirectly via aseg.presurf.mgz.

So doesn't this mean that we should only out the -bigventricles flag for the -autorecon2 stage of recon-all ?

Best,
Matthieu

Le mer. 19 sept. 2018 à 15:17, Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu> a écrit :

Yes - if you've used the -bigventricles flag, you should always include it with the recon-all command.


Bram 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>
Sent: Tuesday, September 18, 2018 12:45:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubles to determine the type of recon editing needed
 

        External Email - Use Caution        

Ok I will test it on normal subjects.

Do I have to put this -bigventricles flag on all recon-all commands following manual editing of brainmask, white matter,...etc or just once at the first recon-all -all command ?

Best,
Matthieu

Le mar. 18 sept. 2018 à 18:03, Bruce Fischl <fischl@nmr.mgh.harvard.edu> a écrit :
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
>
>             The information in this e-mail is intended only for the person to whom it is
>             addressed. If you believe this e-mail was sent to you in error and the
>             e-mail
>             contains patient information, please contact the Partners Compliance
>             HelpLine at
>             http://www.partners.org/complianceline . If the e-mail was sent to you in
>             error
>             but does not contain patient information, please contact the sender and
>             properly
>             dispose of the e-mail.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
>
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.