Saving vector volume in tiff format

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Saving vector volume in tiff format

Ganesh Narayanasamy-2

Hi,
 This is a newbie to Slicer3D. I have attached here a deformation field obtained by registering two CT image volumes using diffeomorphic demons method. This image is a single slice of the original 3D vector volume which is in mha format. I tried converting that into tiff or jpeg or gif format, but it won't. Can you help me interpret this color image.

Thanks,
Ganesh

************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
************************************************************************



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Re: Saving vector volume in tiff format

Andrey Fedorov
Hi Ganesh,

I am not sure Slicer is the best tool for visualizing deformation
fields, at least, not yet.  I would not be attempting to interpret
this image, because it is not clear what is actually shown. Looking at
the range, it seems that the intensity ("color") corresponds to the
displacement of one of the compoents for the displacement field
vectors, but this is just a guess. I am not sure this is of particular
use to you.

There are several tools available for you to visualize deformation
field. You can try paraview (http://paraview.org). It will allow you
to load a deformation field saved as a .mha volume. Next you can
create glyphs from this image. I usually set scaling parameter to 1 to
preserve the values. This will give you displacement vectors. Next you
can visualize the color bar annotated by the magnitude of the the
deformation vectors, which you then can interpret.

Please let us know if these instructions are not sufficient, and I can
try to explain in more detail.

I wish it was this easy to visualize deformation field in Slicer. But
for now it is an open feature request
http://www.na-mic.org/Bug/view.php?id=746

AF



On Thu, Jun 3, 2010 at 16:51, Ganesh Narayanasamy <[hidden email]> wrote:

>
> Hi,
>  This is a newbie to Slicer3D. I have attached here a deformation field
> obtained by registering two CT image volumes using diffeomorphic demons
> method. This image is a single slice of the original 3D vector volume which
> is in mha format. I tried converting that into tiff or jpeg or gif format,
> but it won't. Can you help me interpret this color image.
>
> Thanks,
> Ganesh
>
> ************************************************************************
> "What the mind of man can conceive and believe, It can achieve" - Napolean
> Hill
> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> ************************************************************************
>
>
> ________________________________
> Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.
> Learn more.
> _______________________________________________
> 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: Saving vector volume in tiff format

Ganesh Narayanasamy-2
In reply to this post by Ganesh Narayanasamy-2

Thank you for the immediate reply. That was helpful.
When I tried opening the deformation vector volume in paraview, I could not see anything. Maybe I have to click a few more buttons to view anything. Please find the attachment. Can you help me with using the Paraview 3.8.0 software so that i can view the deformation vector field.

Thanks,
Ganesh

************************************************************************
"What the mind of man can conceive and believe, It can achieve" - Napolean Hill
-Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
Earlier work: http://www.sciencedaily.com/releases/2007/05/070504133017.htm
************************************************************************



> Date: Thu, 3 Jun 2010 17:14:20 -0400
> Subject: Re: [slicer-users] Saving vector volume in tiff format
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> Hi Ganesh,
>
> I am not sure Slicer is the best tool for visualizing deformation
> fields, at least, not yet. I would not be attempting to interpret
> this image, because it is not clear what is actually shown. Looking at
> the range, it seems that the intensity ("color") corresponds to the
> displacement of one of the compoents for the displacement field
> vectors, but this is just a guess. I am not sure this is of particular
> use to you.
>
> There are several tools available for you to visualize deformation
> field. You can try paraview (http://paraview.org). It will allow you
> to load a deformation field saved as a .mha volume. Next you can
> create glyphs from this image. I usually set scaling parameter to 1 to
> preserve the values. This will give you displacement vectors. Next you
> can visualize the color bar annotated by the magnitude of the the
> deformation vectors, which you then can interpret.
>
> Please let us know if these instructions are not sufficient, and I can
> try to explain in more detail.
>
> I wish it was this easy to visualize deformation field in Slicer. But
> for now it is an open feature request
> http://www.na-mic.org/Bug/view.php?id=746
>
> AF
>
>
>
> On Thu, Jun 3, 2010 at 16:51, Ganesh Narayanasamy <[hidden email]> wrote:
> >
> > Hi,
> >  This is a newbie to Slicer3D. I have attached here a deformation field
> > obtained by registering two CT image volumes using diffeomorphic demons
> > method. This image is a single slice of the original 3D vector volume which
> > is in mha format. I tried converting that into tiff or jpeg or gif format,
> > but it won't. Can you help me interpret this color image.
> >
> > Thanks,
> > Ganesh
> >
> > ************************************************************************
> > "What the mind of man can conceive and believe, It can achieve" - Napolean
> > Hill
> > -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> > ************************************************************************
> >
> >
> > ________________________________
> > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox.
> > Learn more.
> > _______________________________________________
> > 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: Saving vector volume in tiff format

Andrey Fedorov
1) once the data is loaded, select the deformation field volume in the
"Pipeline browser", and choose "Filters -> Alphabetical -> Glyph", hit
"Apply" button in Glyph "Properties" panel

2) with Glyph node selected in the pipeline browser, hit "Toggle color
legend visibility" button (the button under "File open" button)




On Mon, Jun 7, 2010 at 10:04, Ganesh Narayanasamy <[hidden email]> wrote:

>
> Thank you for the immediate reply. That was helpful.
> When I tried opening the deformation vector volume in paraview, I could not
> see anything. Maybe I have to click a few more buttons to view anything.
> Please find the attachment. Can you help me with using the Paraview 3.8.0
> software so that i can view the deformation vector field.
>
> Thanks,
> Ganesh
>
> ************************************************************************
> "What the mind of man can conceive and believe, It can achieve" - Napolean
> Hill
> -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
> Earlier work: http://www.sciencedaily.com/releases/2007/05/070504133017.htm
> ************************************************************************
>
>
>
>> Date: Thu, 3 Jun 2010 17:14:20 -0400
>> Subject: Re: [slicer-users] Saving vector volume in tiff format
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Ganesh,
>>
>> I am not sure Slicer is the best tool for visualizing deformation
>> fields, at least, not yet. I would not be attempting to interpret
>> this image, because it is not clear what is actually shown. Looking at
>> the range, it seems that the intensity ("color") corresponds to the
>> displacement of one of the compoents for the displacement field
>> vectors, but this is just a guess. I am not sure this is of particular
>> use to you.
>>
>> There are several tools available for you to visualize deformation
>> field. You can try paraview (http://paraview.org). It will allow you
>> to load a deformation field saved as a .mha volume. Next you can
>> create glyphs from this image. I usually set scaling parameter to 1 to
>> preserve the values. This will give you displacement vectors. Next you
>> can visualize the color bar annotated by the magnitude of the the
>> deformation vectors, which you then can interpret.
>>
>> Please let us know if these instructions are not sufficient, and I can
>> try to explain in more detail.
>>
>> I wish it was this easy to visualize deformation field in Slicer. But
>> for now it is an open feature request
>> http://www.na-mic.org/Bug/view.php?id=746
>>
>> AF
>>
>>
>>
>> On Thu, Jun 3, 2010 at 16:51, Ganesh Narayanasamy <[hidden email]>
>> wrote:
>> >
>> > Hi,
>> >  This is a newbie to Slicer3D. I have attached here a deformation field
>> > obtained by registering two CT image volumes using diffeomorphic demons
>> > method. This image is a single slice of the original 3D vector volume
>> > which
>> > is in mha format. I tried converting that into tiff or jpeg or gif
>> > format,
>> > but it won't. Can you help me interpret this color image.
>> >
>> > Thanks,
>> > Ganesh
>> >
>> > ************************************************************************
>> > "What the mind of man can conceive and believe, It can achieve" -
>> > Napolean
>> > Hill
>> > -Ganesh Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
>> > ************************************************************************
>> >
>> >
>> > ________________________________
>> > Hotmail has tools for the New Busy. Search, chat and e-mail from your
>> > inbox.
>> > Learn more.
>> > _______________________________________________
>> > 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
>> >
>
> ________________________________
> The New Busy is not the too busy. Combine all your e-mail accounts with
> Hotmail. Get busy.
> _______________________________________________
> 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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