Re: How to extract a 2D slice from 3D volume?

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Re: How to extract a 2D slice from 3D volume?

Andrey Fedorov
Alexander,

One way to do this is to use "Create a DICOM Series" module to convert
your 3D image into a series of 2D slices:

http://wiki.slicer.org/slicerWiki/index.php/Modules:CreateaDicomSeries-Documentation-3.6

After this you can use "Add volume" to select an individual slice,
check "Single file" checkbox on the bottom, and load this specific
slice. Then you can save this specific slice as a separate image (nrrd
or whatever you prefer). The limitation of this approach is you will
not be able to choose the axis along which the slices will be
extracted, but I don't see any other Slicer solution right away...

I copy the slicer user list, maybe there are other suggestions. In the
future, I suggest that you send your Slicer user questions to this
list to  get the most complete answer.

AF



On Fri, Sep 10, 2010 at 21:02,  <[hidden email]> wrote:

>
> Dear Andrey,
>
> I try to write one of the slice (for example, order of second slices) into
> the separated files, but I can't find how to do it in 3D Slicer tutorial .
> Would you so kind promt me about this? Thanks.
>
> Best
>
> Alexander
>
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Re: How to extract a 2D slice from 3D volume?

pieper
Administrator
Hi Alexander, Andriy -

This may be a place where you would want to use the Orient Images module:

http://www.slicer.org/slicerWiki/index.php/Modules:OrientImages-Documentation-3.6

-Steve

On Sep/10/10 11:54 PM, Andriy Fedorov wrote:

> Alexander,
>
> One way to do this is to use "Create a DICOM Series" module to convert
> your 3D image into a series of 2D slices:
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:CreateaDicomSeries-Documentation-3.6
>
> After this you can use "Add volume" to select an individual slice,
> check "Single file" checkbox on the bottom, and load this specific
> slice. Then you can save this specific slice as a separate image (nrrd
> or whatever you prefer). The limitation of this approach is you will
> not be able to choose the axis along which the slices will be
> extracted, but I don't see any other Slicer solution right away...
>
> I copy the slicer user list, maybe there are other suggestions. In the
> future, I suggest that you send your Slicer user questions to this
> list to  get the most complete answer.
>
> AF
>
>
>
> On Fri, Sep 10, 2010 at 21:02,<[hidden email]>  wrote:
>>
>> Dear Andrey,
>>
>> I try to write one of the slice (for example, order of second slices) into
>> the separated files, but I can't find how to do it in 3D Slicer tutorial .
>> Would you so kind promt me about this? Thanks.
>>
>> Best
>>
>> Alexander
>>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: How to extract a 2D slice from 3D volume?

Andrey Fedorov
In reply to this post by Andrey Fedorov
On Sat, Sep 11, 2010 at 12:27,  <[hidden email]> wrote:

> Dear Andrey,
>
> Thank you for response.
>
> I confuse,  I was not clear. Let me describe my problem in detail:
>
> 1. I have 500 DICOM files. These are a one of the projection (for
> example on XY plane) of brain vessels's net made by angiogram technology. I
> have the 500 *.jgp  format files of these projections, also.
>
> 2. 3D slicer (or VMTK) automaticaly opens its (500 DICOM files) and gives us
> a three projections (XY, YZ, XZ).
>
> 3. I need a jpg/bmp/png etc.. (or DICOM)  format files of another projection
> (for example YZ), which is shown on one of the (for example, red framed)
> below window of 3D slicer. i.e.  I need to write these projections (500
> slices of YZ projections) in separated files automaticaly.
>
> Does the proposed by your  way do this?
>

Yes, you can first use the Orient Images module suggested by Steve to
change the orientation of the image, and then you can use the Create
DICOM series module to save slices in different projection.

>
> P.S. What do you think, what's the best method to segment the brain
> vessels's net.
>

I don't know what is the best method (and I don't know how you define
"best"). But I know that if you want to do this with Slicer, you
probably need to look at the VMTK extension. Search for the related
components on this page:

http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6

Again, please subscribe to slicer-user list and copy to the list on
all your slicer-related communication. Thank you.


> -----Original Message-----
> From: Andriy Fedorov <[hidden email]>
> To: [hidden email]
> Cc: [hidden email]
> Sent: Fri, Sep 10, 2010 10:54 pm
> Subject: Re: How to extract a 2D slice from 3D volume?
>
> Alexander,
>
> One way to do this is to use "Create a DICOM Series" module to convert
> your 3D image into a series of 2D slices:
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:CreateaDicomSeries-Documentation-3.6
>
> After this you can use "Add volume" to select an individual slice,
> check "Single file" checkbox on the bottom, and load this specific
> slice. Then you can save this specific slice as a separate image (nrrd
> or whatever you prefer). The limitation of this approach is you will
> not be able to choose the axis along which the slices will be
> extracted, but I don't see any other Slicer solution right away...
>
> I copy the slicer user list, maybe there are other suggestions. In the
> future, I suggest that you send your Slicer user questions to this
> list to  get the most complete answer.
>
> AF
>
>
>
> On Fri, Sep 10, 2010 at 21:02,  <[hidden email]> wrote:
>>
>> Dear Andrey,
>>
>> I try to write one of the slice (for example, order of second slices) into
>> the separated files, but I can't find how to do it in 3D Slicer tutorial .
>> Would you so kind promt me about this? Thanks.
>>
>> Best
>>
>> Alexander
>>
>
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: How to extract a 2D slice from 3D volume?

Daniel Haehn
In reply to this post by Andrey Fedorov
Hi alex,

The vmtk in 3d slicer tools really could help you with brain vessel extraction. You should look at VMTKVesselEnhancement and VMTKEasyLevelSetSegmentation.

Perform Frangi vessel enhancement first and then perform the level set initialization on the enhanced image. Then use Geodesic Active Contour evolution on the original image. There are some tutorials available which you can find on the documentation page Andriy mentioned.

Daniel

Andriy Fedorov <[hidden email]> wrote:

>On Sat, Sep 11, 2010 at 12:27,  <[hidden email]> wrote:
>> Dear Andrey,
>>
>> Thank you for response.
>>
>> I confuse,  I was not clear. Let me describe my problem in detail:
>>
>> 1. I have 500 DICOM files. These are a one of the projection (for
>> example on XY plane) of brain vessels's net made by angiogram technology. I
>> have the 500 *.jgp  format files of these projections, also.
>>
>> 2. 3D slicer (or VMTK) automaticaly opens its (500 DICOM files) and gives us
>> a three projections (XY, YZ, XZ).
>>
>> 3. I need a jpg/bmp/png etc.. (or DICOM)  format files of another projection
>> (for example YZ), which is shown on one of the (for example, red framed)
>> below window of 3D slicer. i.e.  I need to write these projections (500
>> slices of YZ projections) in separated files automaticaly.
>>
>> Does the proposed by your  way do this?
>>
>
>Yes, you can first use the Orient Images module suggested by Steve to
>change the orientation of the image, and then you can use the Create
>DICOM series module to save slices in different projection.
>
>>
>> P.S. What do you think, what's the best method to segment the brain
>> vessels's net.
>>
>
>I don't know what is the best method (and I don't know how you define
>"best"). But I know that if you want to do this with Slicer, you
>probably need to look at the VMTK extension. Search for the related
>components on this page:
>
>http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6
>
>Again, please subscribe to slicer-user list and copy to the list on
>all your slicer-related communication. Thank you.
>
>
>> -----Original Message-----
>> From: Andriy Fedorov <[hidden email]>
>> To: [hidden email]
>> Cc: [hidden email]
>> Sent: Fri, Sep 10, 2010 10:54 pm
>> Subject: Re: How to extract a 2D slice from 3D volume?
>>
>> Alexander,
>>
>> One way to do this is to use "Create a DICOM Series" module to convert
>> your 3D image into a series of 2D slices:
>>
>> http://wiki.slicer.org/slicerWiki/index.php/Modules:CreateaDicomSeries-Documentation-3.6
>>
>> After this you can use "Add volume" to select an individual slice,
>> check "Single file" checkbox on the bottom, and load this specific
>> slice. Then you can save this specific slice as a separate image (nrrd
>> or whatever you prefer). The limitation of this approach is you will
>> not be able to choose the axis along which the slices will be
>> extracted, but I don't see any other Slicer solution right away...
>>
>> I copy the slicer user list, maybe there are other suggestions. In the
>> future, I suggest that you send your Slicer user questions to this
>> list to  get the most complete answer.
>>
>> AF
>>
>>
>>
>> On Fri, Sep 10, 2010 at 21:02,  <[hidden email]> wrote:
>>>
>>> Dear Andrey,
>>>
>>> I try to write one of the slice (for example, order of second slices) into
>>> the separated files, but I can't find how to do it in 3D Slicer tutorial .
>>> Would you so kind promt me about this? Thanks.
>>>
>>> Best
>>>
>>> Alexander
>>>
>>
>_______________________________________________
>slicer-users mailing list
>[hidden email]
>http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject