Units of Ruler Tool in 3D Slicer

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Units of Ruler Tool in 3D Slicer

Hannah Dunn

Hi,

Does anyone know what the units are for the measurement given by the ruler tool or what the value corresponds to?

Slicer gives a value followed my 'mm' however millimetres can't be correct for what I'm measuring.

Many Thanks,

Hannah


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Re: Units of Ruler Tool in 3D Slicer

Aucoin, Nicole
Hello Hannah,

The rulers are intended to measure in millimetres, are you seeing
unexpected results in 2D or 3D? Can you share a screen capture and/or a
de-identified data set?

Nicole

On 8/11/14 8:06 AM, Hannah Dunn wrote:

>
> Hi,
>
> Does anyone know what the units are for the measurement given by the
> ruler tool or what the value corresponds to?
>
> Slicer gives a value followed my 'mm' however millimetres can't be
> correct for what I'm measuring.
>
> Many Thanks,
>
> Hannah
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please
> see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm 
> <http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm%20>
>
>
>
>
> _______________________________________________
> 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]
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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: Units of Ruler Tool in 3D Slicer

Hannah Dunn
Hi Nicole,
I've attached a couple of screenshots of one of the measurements.
I've labelled which part I'm trying to measure and the value slicer gives me is 132.4mm. Which is too big for a mouse skull.
However if I multiply this by the pixel size of 41.8 microns (assuming that 132.4 is the pixel number) I get 5.5mm which makes a little more sense.
Many Thanks,
Hannah
________________________________________
From: Nicole Aucoin [[hidden email]]
Sent: 11 August 2014 15:08
To: Hannah Dunn; [hidden email]
Subject: Re: [slicer-users] Units of Ruler Tool in 3D Slicer

Hello Hannah,

The rulers are intended to measure in millimetres, are you seeing
unexpected results in 2D or 3D? Can you share a screen capture and/or a
de-identified data set?

Nicole

On 8/11/14 8:06 AM, Hannah Dunn wrote:

>
> Hi,
>
> Does anyone know what the units are for the measurement given by the
> ruler tool or what the value corresponds to?
>
> Slicer gives a value followed my 'mm' however millimetres can't be
> correct for what I'm measuring.
>
> Many Thanks,
>
> Hannah
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please
> see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm
> <http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm%20>
>
>
>
>
> _______________________________________________
> 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.

This email may have a PROTECTIVE MARKING, for an explanation please see: http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm

_______________________________________________
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ScreenShots.pdf (563K) Download Attachment
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Re: Units of Ruler Tool in 3D Slicer

Murat Maga
Ha ha, welcome to the lovely world of working with mouse imaging in Slicer
:)

You will need to setup the image spacing in your volume (under volumes
module) for the ruler to report your measurements correctly. However, if you
do that you will encounter other issues. You have couple of options.

1. Keep doing what you are doing. It is the simplest solution if you are
working with few samples and if the voxel spacing is not different among
your samples. Very little book keeping.
2. If you a have a lot of samples to process, do enter the correct spacing,
but multiply by 100 if all your volumes are in the range of 40 microns. This
way book keeping is a little simple (you just have to divide the measurement
by 100 to get the correct mm reading).

It is not the ideal solution, but if you enter the correct resolution as it
is you will encounter many other rendering related problems.

Cheers,
Murat

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Hannah Dunn
Sent: Monday, August 11, 2014 8:12 AM
To: Nicole Aucoin; [hidden email]
Subject: Re: [slicer-users] Units of Ruler Tool in 3D Slicer

Hi Nicole,
I've attached a couple of screenshots of one of the measurements.
I've labelled which part I'm trying to measure and the value slicer gives me
is 132.4mm. Which is too big for a mouse skull.
However if I multiply this by the pixel size of 41.8 microns (assuming that
132.4 is the pixel number) I get 5.5mm which makes a little more sense.
Many Thanks,
Hannah
________________________________________
From: Nicole Aucoin [[hidden email]]
Sent: 11 August 2014 15:08
To: Hannah Dunn; [hidden email]
Subject: Re: [slicer-users] Units of Ruler Tool in 3D Slicer

Hello Hannah,

The rulers are intended to measure in millimetres, are you seeing unexpected
results in 2D or 3D? Can you share a screen capture and/or a de-identified
data set?

Nicole

On 8/11/14 8:06 AM, Hannah Dunn wrote:

>
> Hi,
>
> Does anyone know what the units are for the measurement given by the
> ruler tool or what the value corresponds to?
>
> Slicer gives a value followed my 'mm' however millimetres can't be
> correct for what I'm measuring.
>
> Many Thanks,
>
> Hannah
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please
> see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/ind
> ex.htm
> <http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/in
> dex.htm%20>
>
>
>
>
> _______________________________________________
> 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.

This email may have a PROTECTIVE MARKING, for an explanation please see:
http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm

_______________________________________________
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: Units of Ruler Tool in 3D Slicer

Julien Finet
Hi Hannah,

Units have been improved in Slicer in the past months. However, as you experienced it, some issues remain when dealing with microscopic scales.
I will be looking at your specific issues next week. I'll be contacting you if I need more information on your side.

Please let us know if you have any question.

Thanks,
Julien.


On Mon, Aug 11, 2014 at 12:29 PM, Murat Maga <[hidden email]> wrote:
Ha ha, welcome to the lovely world of working with mouse imaging in Slicer
:)

You will need to setup the image spacing in your volume (under volumes
module) for the ruler to report your measurements correctly. However, if you
do that you will encounter other issues. You have couple of options.

1. Keep doing what you are doing. It is the simplest solution if you are
working with few samples and if the voxel spacing is not different among
your samples. Very little book keeping.
2. If you a have a lot of samples to process, do enter the correct spacing,
but multiply by 100 if all your volumes are in the range of 40 microns. This
way book keeping is a little simple (you just have to divide the measurement
by 100 to get the correct mm reading).

It is not the ideal solution, but if you enter the correct resolution as it
is you will encounter many other rendering related problems.

Cheers,
Murat

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Hannah Dunn
Sent: Monday, August 11, 2014 8:12 AM
To: Nicole Aucoin; [hidden email]
Subject: Re: [slicer-users] Units of Ruler Tool in 3D Slicer

Hi Nicole,
I've attached a couple of screenshots of one of the measurements.
I've labelled which part I'm trying to measure and the value slicer gives me
is 132.4mm. Which is too big for a mouse skull.
However if I multiply this by the pixel size of 41.8 microns (assuming that
132.4 is the pixel number) I get 5.5mm which makes a little more sense.
Many Thanks,
Hannah
________________________________________
From: Nicole Aucoin [[hidden email]]
Sent: 11 August 2014 15:08
To: Hannah Dunn; [hidden email]
Subject: Re: [slicer-users] Units of Ruler Tool in 3D Slicer

Hello Hannah,

The rulers are intended to measure in millimetres, are you seeing unexpected
results in 2D or 3D? Can you share a screen capture and/or a de-identified
data set?

Nicole

On 8/11/14 8:06 AM, Hannah Dunn wrote:
>
> Hi,
>
> Does anyone know what the units are for the measurement given by the
> ruler tool or what the value corresponds to?
>
> Slicer gives a value followed my 'mm' however millimetres can't be
> correct for what I'm measuring.
>
> Many Thanks,
>
> Hannah
>
>
> This email may have a PROTECTIVE MARKING, for an explanation please
> see:
> http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/ind
> ex.htm
> <http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/in
> dex.htm%20>
>
>
>
>
> _______________________________________________
> 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.

This email may have a PROTECTIVE MARKING, for an explanation please see:
http://www.mrc.ac.uk/About/Informationandstandards/Documentmarking/index.htm

_______________________________________________
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]
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.