Hi Matthieu
only recon2 will use it, but you can specify it for all of them
cheers
Bruce
On Wed, 19 Sep 2018, Matthieu Vanhoutte wrote:
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 <brdiam...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on
behalf of Matthieu Vanhoutte <matthieuvanhou...@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 <fis...@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 <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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