Merging segmentation data into one file?

[Guy]

In error, I segmented two regions of the same greyscale series into 2
different segmentation files. Is there a way to merge the 2
segmentation files so the 2 segmented regions are in the same file?

[Paul Yushkevich]

Yes you can do it in c3d.

C3d a.nii b.nii -replace 1 2 -add -o c.nii

Sent from my iPod

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[Guy]

Thanks. I'm still using v1.8. Can I still use c3d?

Guy

On Sep 20, 10:28 pm, Paul Yushkevich <pyushkev...@gmail.com> wrote:
> Yes you can do it in c3d.
>
> C3d a.nii b.nii -replace 1 2 -add -o c.nii
>
> Sent from my iPod
>

[Paul Yushkevich]

Sure, they are separate downloads (c3d is at itksnap.org/c3d)

Is 2.0 giving you trouble, or are you sticking to 1.8 for protocol consistency?

Paul.

--
Paul A. Yushkevich, Ph.D.
Assistant Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Guy]

Protocol consistency.

>C3d a.nii b.nii -replace 1 2 -add -o c.nii

I assume a.nii and b.nii are the two files I wish to combine, and
c.nii is the name I want to give to the new file that now has the
combined data. Is that correct.

Also, do 1 2 represent the label IDs of the regions I wish to
combine? In my OP, for simplicity I said there were 2 regions, but
there are actually 5 regions...2 regions on one file and 3 on the
other. So if my regions I want in the combined file are labeled 1, 3,
4, 6 and 7 then I would write: C3d a.nii b.nii -replace 1 3 4 6 7 -
add -o c.nii ?

I'm not real experienced with using cmd, so I hope my questions aren't
too basic. But, will the a.nii and b.nii files be affected at all in
creating the c.nii file? Also, do the a.nii and b.nii files need to
be in the folder c3d-0.8.2\bin?

Thanks,
Guy

On Sep 23, 7:16 pm, Paul Yushkevich <pau...@mail.med.upenn.edu> wrote:
> Sure, they are separate downloads (c3d is at itksnap.org/c3d)
>
> Is 2.0 giving you trouble, or are you sticking to 1.8 for protocol
> consistency?
>
> Paul.
>
>
>
> On Thu, Sep 23, 2010 at 11:06 AM, Guy <glombard...@optonline.net> wrote:
> > Thanks.  I'm still using v1.8.  Can I still use c3d?
>
> > Guy
>
> > On Sep 20, 10:28 pm, Paul Yushkevich <pyushkev...@gmail.com> wrote:
> > > Yes you can do it in c3d.
>
> > > C3d a.nii b.nii -replace 1 2 -add -o c.nii
>
> > > Sent from my iPod
>
> > > On Sep 21, 2010, at 9:41 AM, Guy <glombard...@optonline.net> wrote:
>
> > > > In error, I segmented two regions of the same greyscale series into 2
> > > > different segmentation files.  Is there a way to merge the 2
> > > > segmentation files so the 2 segmented regions are in the same file?
>
> > > > --
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[Paul Yushkevich]

Hi

>C3d a.nii b.nii -replace 1 2 -add -o c.nii

this command means

- load a

- load b

- replace label 1 in b with label 2

- add a and b and save as c

(see itksnap.org/c3d for documentation)

Now let's say you have in a.nii label 1 for left hippo, 2 for left amygdala, 3 for left thalamus and in b.nii you have 1 for right hippo, 2 for left amygdala, etc. Run

c3d a.nii b.nii -replace 1 4 2 5 3 6 -add -o c.nii

or

c3d a.nii b.nii -shift 4 -add -o c.nii

Paul

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[Guy]

OK, I think I get it. So that means if label 1 is left hippo, 2 is
left amygdala,
3 is left thalamus, and if in a.nii I segmented 1 and 2, and in b.nii
I segmented 3, then I would run

c3d a.nii b.nii -add -o c.nii ? Is that right?

Thanks,
Guy

> > <itksnap-users%2Bunsu...@googlegroups.com<itksnap-users%252Buns...@googlegroups.com>

>
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[Pokorny, Saskia]

Hello together,

 

I am just starting to use ITK snap and was wondering, if it is possible to manually select a couple of slices that define regions the automatic selection has to meet? (I do not want to use the manual selected regions as starting point for the snake, rather I would like that they present boundary conditions for my snake in the automatic selction?). This would be of great help to me.

I am trying to create a model of the different regions of the heart (ventricle, atrium, myocardium) using ITK Snap. At the moment I am always having the problem, that the contrast between the different regions is very low. Therefore I was not able to successfully segmentat the different regions until now. I would appreciate any kind of help or ideas very much!

 

Best Regards

 

Saskia

 

 

 

Dipl. Ing. Saskia Pokorny

Lehrstuhl für Experimentelle

Herzchirurgie und Herzklappenersatz

UKSH, Campus Kiel

Klinik für Herz- und Gefäßchirurgie

Arnold-Heller-Str.3, Hs 17

D-24105 Kiel

 

Tel: +49 431 597 5010

Fax: +49 431 597 4249

E-Mail: saskia....@uksh-kiel.de

 

 

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[Paul Yushkevich]

Hi Saskia

That's not presently a feature, unfortunately. You can however, mask your segmentation with hand segmentations. You can draw some polygons to define your region of interest with label 2. Then before running automatic segmentation, select label 1 as the "drawing label" and label 2 as the "draw over" label. This way, when you "finish" your active contour segmentation, it will only be applied to the voxels that have label 2. You would need to label the ROI on every slice where you want to run active contours, but you can do this quickly in polygon mode using the "paste" button.

Hope this helps!

Paul.

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[Runa Unsgård]

Hi!

I made the same error. Is there a way to merge the segmentation files into one file in the itk snap program?

Runa

[Paul Yushkevich]

Yes, it is easy to do with c3d, please see above for examples of using c3d to merge labels between multiple files.

Paul

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--

Paul A. Yushkevich, Ph.D.
Professor of Radiology

Penn Image Computing and Science Laboratory

University of Pennsylvania Perelman School of Medicine