Adjusting Image Dimensions

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Adjusting Image Dimensions

Strugari, Matthew SCA
Hi Slicer users,

Is anyone aware of any method that can be used to manually define volume dimensions? I am attempting to export a DICOM/RT Structure set but I am receiving an error stating "Image size mismatch when adding structure". It is caused by my labelmap which has dimensions 205x190x36 while my US volume has dimenions 636x476x64. I would essentially like to extend the background of my labelmap so that the volume dimensions are the same as that for the US image. Is this possible while maintaining the current position of the labelmap in relation to the US image?

Matthew
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Re: Adjusting Image Dimensions

Bradley Lowekamp
Hello,

If the images are ready occupy the same physical location by having the same space, origin, and orientation then simply just padding is what you need.

In the SimpleFilters module search for Pad. You likely want the constant pad filter. Should be straight forward enough to use.

Brad

On Oct 7, 2014, at 1:17 PM, Strugari, Matthew SCA <[hidden email]> wrote:

> Hi Slicer users,
>
> Is anyone aware of any method that can be used to manually define volume dimensions? I am attempting to export a DICOM/RT Structure set but I am receiving an error stating "Image size mismatch when adding structure". It is caused by my labelmap which has dimensions 205x190x36 while my US volume has dimenions 636x476x64. I would essentially like to extend the background of my labelmap so that the volume dimensions are the same as that for the US image. Is this possible while maintaining the current position of the labelmap in relation to the US image?
>
> Matthew
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>

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Re: Adjusting Image Dimensions

Andras Lasso-2
If origin, spacing, or direction is not exactly the same then you can use one of the resample volume modules with nearest neighbor interpolation. As a result you'll get a new volume that exactly matches the geometry of the reference volume.

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Bradley Lowekamp
Sent: Tuesday, October 07, 2014 1:30 PM
To: Strugari, Matthew SCA
Cc: [hidden email]
Subject: Re: [slicer-users] Adjusting Image Dimensions

Hello,

If the images are ready occupy the same physical location by having the same space, origin, and orientation then simply just padding is what you need.

In the SimpleFilters module search for Pad. You likely want the constant pad filter. Should be straight forward enough to use.

Brad

On Oct 7, 2014, at 1:17 PM, Strugari, Matthew SCA <[hidden email]> wrote:

> Hi Slicer users,
>
> Is anyone aware of any method that can be used to manually define volume dimensions? I am attempting to export a DICOM/RT Structure set but I am receiving an error stating "Image size mismatch when adding structure". It is caused by my labelmap which has dimensions 205x190x36 while my US volume has dimenions 636x476x64. I would essentially like to extend the background of my labelmap so that the volume dimensions are the same as that for the US image. Is this possible while maintaining the current position of the labelmap in relation to the US image?
>
> Matthew
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> The information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in error
> and the e-mail contains patient information, please contact the
> Partners Compliance HelpLine at http://www.partners.org/complianceline 
> . If the e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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Re: Adjusting Image Dimensions

Julien Finet
You could also create an image of the size you want using the ImageMaker extension, initialized with 0s. And with the "Add Scalar Volume" module add your labelmap into the created image.
Hth,
Julien.

On Tue, Oct 7, 2014 at 1:36 PM, Andras Lasso <[hidden email]> wrote:
If origin, spacing, or direction is not exactly the same then you can use one of the resample volume modules with nearest neighbor interpolation. As a result you'll get a new volume that exactly matches the geometry of the reference volume.

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Bradley Lowekamp
Sent: Tuesday, October 07, 2014 1:30 PM
To: Strugari, Matthew SCA
Cc: [hidden email]
Subject: Re: [slicer-users] Adjusting Image Dimensions

Hello,

If the images are ready occupy the same physical location by having the same space, origin, and orientation then simply just padding is what you need.

In the SimpleFilters module search for Pad. You likely want the constant pad filter. Should be straight forward enough to use.

Brad

On Oct 7, 2014, at 1:17 PM, Strugari, Matthew SCA <[hidden email]> wrote:

> Hi Slicer users,
>
> Is anyone aware of any method that can be used to manually define volume dimensions? I am attempting to export a DICOM/RT Structure set but I am receiving an error stating "Image size mismatch when adding structure". It is caused by my labelmap which has dimensions 205x190x36 while my US volume has dimenions 636x476x64. I would essentially like to extend the background of my labelmap so that the volume dimensions are the same as that for the US image. Is this possible while maintaining the current position of the labelmap in relation to the US image?
>
> Matthew
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> The information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in error
> and the e-mail contains patient information, please contact the
> Partners Compliance HelpLine at http://www.partners.org/complianceline
> . If the e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>

_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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Re: Adjusting Image Dimensions

Strugari, Matthew SCA
In reply to this post by Andras Lasso-2
Hi Brad and Andras,

The image spacing was the same between the labelmap and US image but the origins were different. Andras' method was exactly what I was looking for.

Thanks for the help! It is greatly appreciated!

Matthew
________________________________________
From: Andras Lasso [[hidden email]]
Sent: October 7, 2014 11:36 AM
To: Bradley Lowekamp; Strugari, Matthew SCA
Cc: [hidden email]
Subject: RE: [slicer-users] Adjusting Image Dimensions

If origin, spacing, or direction is not exactly the same then you can use one of the resample volume modules with nearest neighbor interpolation. As a result you'll get a new volume that exactly matches the geometry of the reference volume.

Andras

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Bradley Lowekamp
Sent: Tuesday, October 07, 2014 1:30 PM
To: Strugari, Matthew SCA
Cc: [hidden email]
Subject: Re: [slicer-users] Adjusting Image Dimensions

Hello,

If the images are ready occupy the same physical location by having the same space, origin, and orientation then simply just padding is what you need.

In the SimpleFilters module search for Pad. You likely want the constant pad filter. Should be straight forward enough to use.

Brad

On Oct 7, 2014, at 1:17 PM, Strugari, Matthew SCA <[hidden email]> wrote:

> Hi Slicer users,
>
> Is anyone aware of any method that can be used to manually define volume dimensions? I am attempting to export a DICOM/RT Structure set but I am receiving an error stating "Image size mismatch when adding structure". It is caused by my labelmap which has dimensions 205x190x36 while my US volume has dimenions 636x476x64. I would essentially like to extend the background of my labelmap so that the volume dimensions are the same as that for the US image. Is this possible while maintaining the current position of the labelmap in relation to the US image?
>
> Matthew
> _______________________________________________
> 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
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> The information in this e-mail is intended only for the person to whom
> it is addressed. If you believe this e-mail was sent to you in error
> and the e-mail contains patient information, please contact the
> Partners Compliance HelpLine at http://www.partners.org/complianceline
> . If the e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>

_______________________________________________
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 http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ