[slicer-users] manual segmentation or automatc segmentation

Yi Gao yi.gao at gatech.edu
Sat Dec 18 15:53:38 EST 2010


Hi H.B,

No problem, glad that I can help.

You can see the image information in Slicer like this:

When you load the nrrd file into Slicer,
1. select the "Volume" module, as shown in the red box of the attached figure.
2. select the nrrd file you want to segment in the green box
3. then the blue box shows the pixel-size of the image
4. and the orange box shows the spacing of the image in each direction

Could I get those numbers?

Thanks!

Best,
yi

2010/12/18 H B <r44cd at hotmail.com>:
> Hi Yi,
>
> i dont know how to know the pixel size, but i think this is the width and
> hight of the image,
> now there is 254slics.
> i guss the spassing 1,1,0.6 (as the best view -as i see-)
>
> i am  beginer, so if you have any advice dont hasitate,
>
> thank you very much for your intrest in my work
>
> H.B
>
>> Date: Sat, 18 Dec 2010 15:36:19 -0500
>> Subject: Re: [slicer-users] manual segmentation or automatc segmentation
>> From: yi.gao at gatech.edu
>> To: r44cd at hotmail.com
>> CC: slicer-users at bwh.harvard.edu
>>
>> Hi H.B,
>>
>> Thanks for the info. Does 287*170 mean the size of each axial slice?
>> How many slices do you have in the nrrd file? When you were stacking
>> the png files from the VHP data set, to form a nrrd file, what spacing
>> information did you give in the nrrd file?
>>
>> If you could paste the nrrd file header text here, that would give us
>> more information.
>>
>>
>> Thanks!
>> yi
>>
>> 2010/12/18 H B <r44cd at hotmail.com>:
>> > Hi Yi,
>> >
>> > The size now 36 KB (287x 170) png format
>> > then i transform it to nrrd for editing
>> > the images from visible human project
>> >
>> > it this eno uph information?
>> >
>> > shoud the seeds be more than this and in different slics?
>> >
>> > Thanks,
>> >   H.B
>> >
>> >> Date: Sat, 18 Dec 2010 15:17:16 -0500
>> >> Subject: Re: [slicer-users] manual segmentation or automatc
>> >> segmentation
>> >> From: yi.gao at gatech.edu
>> >> To: r44cd at hotmail.com
>> >>
>> >> what image modality, what's its size?
>> >> usually I used a smaller brash radius, like 1, but 3 should be fine
>> >>
>> >>
>> >>
>> >> 2010/12/18 H B <r44cd at hotmail.com>:
>> >> > i just choose the prush tool(size 3) and click in the liver (spots
>> >> > -circule-) maybe 10 spots only.
>> >> >
>> >> > do you have any advice?
>> >> >
>> >> > Regards
>> >> >
>> >> > H.B
>> >> >
>> >> >> Date: Sat, 18 Dec 2010 09:22:58 -0500
>> >> >> Subject: Re: [slicer-users] manual segmentation or automatc
>> >> >> segmentation
>> >> >> From: yi.gao at gatech.edu
>> >> >> To: r44cd at hotmail.com
>> >> >> CC: slicer-users at bwh.harvard.edu
>> >> >>
>> >> >> Hi H.B,
>> >> > >
>> >> >> setting boundary smoothness to 1 should give very smooth/spherical
>> >> >> boundary, or even shrink the surface to a more spherical object....
>> >> >> How is the initial label(seed) map? Could you show three standard
>> >> >> views of the input label? (The "ar" volume in your screen shot) How
>> >> >> large is the data set and how long, roughly, does it take to compute
>> >> >> the result?
>> >> >>> >> >> Thanks,
>> >> >> yi
>> >> >>
>> >> >> On Fri, Dec 17, 2010 at 2:16 PM, Yi Gao <yi.gao at gatech.edu> wrote:
>> >> >> > Hi H.B
>> >> >> >
>> >> >> > Could I know your chose of the "Boundary Smoothness" parameter?
>> >> >> > Does
>> >> >> > increasing that make the result smoother?
>> >> >> >
>> >> >> >
>> >> >> & gt; Thanks,
>> >> >> > yi
>> >> >> >
>> >> >> > 2010/12/1 7 Ron Kikinis <kikinis at bwh.harvard.edu>:
>> >> >> >>
>> >> >> >>
>> >> >> >> -------- Original Message --------
>> >> >> >> Subject:        [slicer-users] manual segmentation or automatc
>> >> >> >> segmenta tion
>> >> >> >> Date:   Fri, 17 Dec 2010 21:41:36 +0300
>> >> >> >> From:   H B <r44cd at hotmail.com>
>> >> >> >> To:     <slicer-users at bwh.harvard.edu>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> Hi all,
>> >> >> >>
>> >> >> >> i am now segment liver and some nigborhoding organs, the time is
>> >> >> >> not
>> >> >> >> important to me as smoth and realistic,
>> >> >> >>
>> >> >> >> i use rubost static segmentation but it were not accurate enough.
>> >> >> >> so
>> >> >> >> i
>> >> >> >> try to corre ct it manually
>> >> >> >>
>> >> >> >> but i am not happy by the result (in the following link)
>> >> >> &g t;> http://up.arab-x.com/Dec10/jhG11086.jpg
>> >> >> >>
>> >> >> >> near to S the manual modification but it is not smooth
>> >> >> >>
>> >> >> >> any advice will be appreciated
>> >> >> >>
>> >> >> >>
>> >> >> >> Regards
>> >> >> >>
>> >> >> >> H.B
>> >> >> >>
>> >> >> >
>> >> >
>> >
>
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