adding new Volume reader

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adding new Volume reader

Simon Drouin
I want to add functionality to Slicer3 to be able to read the MINC file format (volumetric data. For more details: http://en.wikibooks.org/wiki/MINC).

Slicer doesn't seem to support the concept of an importer (am I right?). If it is the case, then what is the way to go? I though of creating a command-line program that converts MINC into a volume format that is supported by Slicer and then create a plugin out of it, but I don't like the idea.

Any suggestions or examples that might help?

Thanks in advance.

s.

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Re: adding new Volume reader

Aucoin, Nicole
This is a question for the slicer-devel mailing list...

Simon Drouin wrote:

> I want to add functionality to Slicer3 to be able to read the MINC
> file format (volumetric data. For more details:
> http://en.wikibooks.org/wiki/MINC).
>
> Slicer doesn't seem to support the concept of an importer (am I
> right?). If it is the case, then what is the way to go? I though of
> creating a command-line program that converts MINC into a volume
> format that is supported by Slicer and then create a plugin out of it,
> but I don't like the idea.
>
> Any suggestions or examples that might help?
>
> Thanks in advance.
>
> s.
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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: adding new Volume reader

pieper
Administrator
In reply to this post by Simon Drouin
Hi Simon -

That sounds like a good thing to have - slicer uses the ITK IO factory
for reading and writing, and it may be that this existing code could be
plugged in directly?

http://www.insight-journal.org/browse/publication/64

If so, that should support scalar volume data directly into slicer.

If something more complicated than scalars is needed (perhaps lookup
tables? mulitple volumes?), then some extra code is probably needed.
The most general way might be to write a converter that exports a MRML
scene that could be imported into slicer.  If it is written as a command
line module, then it could be useful inside slicer or as a stand alone
executable.

Best,
Steve


On May/27/10 2:12 PM, Simon Drouin wrote:

> I want to add functionality to Slicer3 to be able to read the MINC file
> format (volumetric data. For more details:
> http://en.wikibooks.org/wiki/MINC).
>
> Slicer doesn't seem to support the concept of an importer (am I right?).
> If it is the case, then what is the way to go? I though of creating a
> command-line program that converts MINC into a volume format that is
> supported by Slicer and then create a plugin out of it, but I don't like
> the idea.
>
> Any suggestions or examples that might help?
>
> Thanks in advance.
>
> s.
>
>
>
> _______________________________________________
> 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: adding new Volume reader

Sharp, Gregory C.

Hi,

I will further note that ITK has an "advanced option":

ITK_USE_MINC2

-Greg


On Thu, 27 May 2010 14:45:12 -0400
Steve Pieper <[hidden email]> wrote:

> Hi Simon -
>
> That sounds like a good thing to have - slicer uses the ITK IO factory
> for reading and writing, and it may be that this existing code could be
> plugged in directly?
>
> http://www.insight-journal.org/browse/publication/64
>
> If so, that should support scalar volume data directly into slicer.
>
> If something more complicated than scalars is needed (perhaps lookup
> tables? mulitple volumes?), then some extra code is probably needed.
> The most general way might be to write a converter that exports a MRML
> scene that could be imported into slicer.  If it is written as a command
> line module, then it could be useful inside slicer or as a stand alone
> executable.
>
> Best,
> Steve
>
>
> On May/27/10 2:12 PM, Simon Drouin wrote:
> > I want to add functionality to Slicer3 to be able to read the MINC file
> > format (volumetric data. For more details:
> > http://en.wikibooks.org/wiki/MINC).
> >
> > Slicer doesn't seem to support the concept of an importer (am I right?).
> > If it is the case, then what is the way to go? I though of creating a
> > command-line program that converts MINC into a volume format that is
> > supported by Slicer and then create a plugin out of it, but I don't like
> > the idea.
> >
> > Any suggestions or examples that might help?
> >
> > Thanks in advance.
> >
> > s.
> >
> >
> >
> > _______________________________________________
> > 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


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital
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Re: adding new Volume reader

Simon Drouin
Is it as easy as enabling ITK_USE_MINC2 in the ITK build and recompiling? I will try that and let you know.

s.

On Thu, May 27, 2010 at 4:37 PM, Gregory Sharp <[hidden email]> wrote:

Hi,

I will further note that ITK has an "advanced option":

ITK_USE_MINC2

-Greg


On Thu, 27 May 2010 14:45:12 -0400
Steve Pieper <[hidden email]> wrote:

> Hi Simon -
>
> That sounds like a good thing to have - slicer uses the ITK IO factory
> for reading and writing, and it may be that this existing code could be
> plugged in directly?
>
> http://www.insight-journal.org/browse/publication/64
>
> If so, that should support scalar volume data directly into slicer.
>
> If something more complicated than scalars is needed (perhaps lookup
> tables? mulitple volumes?), then some extra code is probably needed.
> The most general way might be to write a converter that exports a MRML
> scene that could be imported into slicer.  If it is written as a command
> line module, then it could be useful inside slicer or as a stand alone
> executable.
>
> Best,
> Steve
>
>
> On May/27/10 2:12 PM, Simon Drouin wrote:
> > I want to add functionality to Slicer3 to be able to read the MINC file
> > format (volumetric data. For more details:
> > http://en.wikibooks.org/wiki/MINC).
> >
> > Slicer doesn't seem to support the concept of an importer (am I right?).
> > If it is the case, then what is the way to go? I though of creating a
> > command-line program that converts MINC into a volume format that is
> > supported by Slicer and then create a plugin out of it, but I don't like
> > the idea.
> >
> > Any suggestions or examples that might help?
> >
> > Thanks in advance.
> >
> > s.
> >
> >
> >
> > _______________________________________________
> > 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


--
Greg Sharp, PhD
Department of Radiation Oncology
Massachusetts General Hospital


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