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 CautionOk 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 CautionHi 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 withmy specific
subject. Not only, this took into account large ventricles but also corrected grey mattersegmentation
from extra Dura tissue that was erroneously segmented in GM. I understand the first point of amelioration allowed by theflag but don't
understand where the second point come from ? If I used the -bigventricles flag for all my atrophied andlarge ventricles
patients and not for my healthy patients, wouldn't it introduce a bias when furtherstatistically
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 thesubject through
recon-all with the -bigventricles flag since it looks like thelateral ventricle was
significantly mislabeled in the aseg. If using the -bigventriclesflag doesn't fix
your problem, you can edit the aseg.mgz manually by following thedirections 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 suggestedin 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 ofrecon editing needed
Hi Matthieu, I've taken a look through the files you shared with us and Isee the poor
surfaces in the posterior right hemisphere you were referring to in yourmessage. It looks
like your subject has a combination of abnormally large ventricles andsignificant wm
abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing thewm.mgz to more
accurately represent the wm from slice 84 to 39. You can take a look at the whitematter 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 labelingthe right lateral
ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain sinceyou didn't send
us the surfaces for the left hemisphere. Before you do that, edit the wm.mgzas 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 theperson to whom it is
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