[slicer-users] Get bones in 3D slicer

Madan Rao rao.lms at gmail.com
Sun Feb 14 03:04:23 EST 2010


Hello all,

Fred's query is translated by my daughter (a high school student):

I started the smoothing of my volumes. Module cast works. When
I arrive in module to guassian blur, I enter the quality-label drawn before
with implicit right-angled. I leave the value sigma has 1, because I do not
know
for what it serves. Module runs, but " with error " and I cannot
safeguard the resultant volume. You seem to have a long experience.
Have you an idea which explains this?

A.M.Mohan Rao

On Sat, Feb 13, 2010 at 11:06 PM, Sylvain Jaume <sylvain at csail.mit.edu>wrote:

> Hi Fred,
>
> I CC slicer-users on this email as other users may benefit from it.
> Please write in English...
>
> To use the GaussianBlur module, you need to set the Input Volume to
> the results of CastImage and to set the Output Volume to 'Create New
> Volume'. You can leave Sigma (standard deviation) to its default value
> 1.
>
> Let me know if you have any issue.
> Sylvain
>
> On Sat, Feb 13, 2010 at 11:49 AM, Fred <fredlouazel at hotmail.com> wrote:
> > Salut Sylvain,
> >
> > J'ai débuté le lissage de mes volumes. Le module cast fonctionne. Lorsque
> > j'arrive dans le module guassian blur, j'entre le label dessiné
> précédemment
> > avec implicite rectangle. Je laisse la valeur sigma a 1 , car je ne sais
> pas
> > à quoi elle sert. Le module roule, mais "avec erreur" et je ne peux pas
> > sauvegarder le volume résultant. Tu sembles avoir une longue expérience.
> > As-tu une idée qui explique ça ?
> >
> > Un gros merci
> >
> > Fred
>
> On Thu, Feb 11, 2010 at 1:40 AM, Sylvain Jaume <sylvain at csail.mit.edu>
> wrote:
> > Hi Fred,
> >
> > You can do everything with Slicer. Just use these modules in this
> sequence:
> >
> > 1. Cast Image: select output type 'float'
> > 2. Gaussian Blur
> > 3. Gray Scale Model Maker: set the value to half the label value (e.g.
> > if label=3, set value=1.5)
> >
> > Regards,
> > Sylvain
> >
> > On Thu, Feb 11, 2010 at 1:07 AM, Fred <fredlouazel at hotmail.com> wrote:
> >> Hi !
> >>
> >> I use different Editor tools to improve the segmentation. Like you
> affirme,
> >> I realy use implicit rectangle to segment but I use the threshold
> fonction
> >> only.
> >>
> >> Now I have to smooth each surface before the meshing step.
> >>
> >> Do you have any idea about how to smooth surface in 3dslicer or other
> >> software ?
> >>
> >> Thank you very much for your help, all things setup very quickly because
> of
> >> you
> >>
> >> Best regards
> >>
> >> Fred
> >>
> >> --------------------------------------------------
> >> From: "Sylvain Jaume" <sylvain at csail.mit.edu>
> >> Sent: Tuesday, February 09, 2010 10:56 AM
> >> To: "Fred L" <fredlouazel at hotmail.com>
> >> Cc: <slicer-users at bwh.harvard.edu>
> >> Subject: Re: [slicer-users] Get bones in 3D slicer
> >>
> >>> Hi Fred,
> >>>
> >>> The screenshots you sent me indicate that you use the Implicit
> >>> Rectangle over the entire slice. Is that correct? You can define
> >>> different 'boxes' using the Implicit Rectangle over different 2D
> >>> regions. Additionally you can change the label value, let's say label
> >>> = 1 for the clavicle and label = 2 for scapula. To apply touch-ups on
> >>> the segmentation results you can use the Paint tool (icon showing a
> >>> paintbrush) and set the radius down to 1 on the left panel. The Editor
> >>> module (by Steve Pieper) contains many interactive segmentation tools
> >>> that you will find very intuitive.
> >>>
> >>> Regards,
> >>> Sylvain
> >>>
> >>> On Tue, Feb 9, 2010 at 10:10 AM, Fred L <fredlouazel at hotmail.com>
> wrote:
> >>>>
> >>>> Hi,
> >>>> I joint a document in which I describe the difference.Thanks for all
> >>>> support
> >>>> you have given to me.
> >>>> Fred
> >>>> ________________________________
> >>>> From: Sylvain Jaume
> >>>> To: Fred Louazel
> >>>> Subject: Re: [slicer-users] Get bones in 3D slicer
> >>>> Date: Mon, 8 Feb 2010 00:52:59 -0500
> >>>> CC: slicer-users at bwh.harvard.edu
> >>>>
> >>>> Hello Fred,
> >>>> If you have a CT scan, you will be able to get an accurate
> segmentation
> >>>> using the Editor module and the implicit segmentation icon. You need
> to
> >>>> set
> >>>> the range of Hounsfield values that correspond to the bone
> intensities.
> >>>> In
> >>>> case that does not produce a satisfying result, would you mind sending
> a
> >>>> screenshot of what you obtain with Slicer and what you obtain with the
> >>>> other
> >>>> software packages?
> >>>>
> >>>> Sylvain
> >>>> On Feb 7, 2010, at 11:41 PM, "Fred" <fredlouazel at hotmail.com> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> In other dicom viewer software, It's possible to view automatically a
> 3D
> >>>> bones model. In 3d slicer, from now, I am only able to get a 3d bone
> >>>> model
> >>>> using the threshold function. Because it a manual segmentation it's
> not
> >>>> as
> >>>> precise as what I got with others softare. Cause I am a newby in
> >>>> 3dSlicer, I
> >>>> sure I can do better . My goal: get a humerus model, a scapula model
> (a
> >>>> segemented 3d model of the shoulder)
> >>>>
> >>>> Does anybody have an idea?
> >>>>
> >>>> Any suggestion would be appreciate
> >>>>
> >>>> Best regards
> >>>>
> >>>> Fred
> >>>>
> >>>> _______________________________________________
> >>>> slicer-users mailing list
> >>>> slicer-users at bwh.harvard.edu
> >>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >>>> To unsubscribe: send email to
> >>>> slicer-users-request at massmail.spl.harvard.edu
> >>>> with unsubscribe as the subject
> >>>>
> >>>> ________________________________
> >>>> Windows® phone-your Windows stuff, on the go. See more.
> >>
> >
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