Save editable intensity range for segments?

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Save editable intensity range for segments?

Hollister Herhold
Hi,

I’m a relatively new Slicer user (6 months or so), using Slicer to segment micro-CT scans of fossil insects. The scans usually have a fairly wide range of intensities depending on the specimen involved - for example, specimens in different types of amber can have vastly different intensity ranges, so I spend a lot of time tweaking intensity ranges and using Sphere brush with editable intensity ranges for different segments.

I was wondering if there is a way to save the intensity range last used for a given segment. Thus far I’ve resorted to just manually noting the intensity range used in the name of a segment, such as “Thorax muscle - 28.2k-max” or “Abdomen cuticle 14.4k-22.7k”. It would be a useful time saver to be able to switch to a segment and have it remember the editable intensity range last used for that segment.

If this doesn’t exist, I was considering looking into adding it. I have a software engineering/programming background and I’m happy to learn enough to be able to add this, but I wanted to make sure this didn’t already exist buried somewhere, or that someone else wasn’t already working on something like this.

Thanks in advance!

-Hollister


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Re: Save editable intensity range for segments?

lasso2

This is exactly what masking options in the Segment Editor is developed for.

 

The idea is that you create a “mask segment” for each tissue type with the threshold effect. The mask is a regular segment, that you select in the masking section as editable region (you'll be able to paint only inside the mask). Make sure disable overwriting segments (or hide the mask segment and choose to overwrite only visible segments).

 

I would also strongly suggest to try “grow from seeds” effect, as it makes segmentation incredibly fast and easy if you have enough intensity difference between your segments.

 

Use the latest nightly build of Slicer, as it contains many fixes and improvements compared to the latest stable version.

 

Andras

 

From: [hidden email]
Sent: Thursday, April 6, 2017 10:43 AM
To: [hidden email]
Subject: [slicer-devel] Save editable intensity range for segments?

 

Hi,

I’m a relatively new Slicer user (6 months or so), using Slicer to segment micro-CT scans of fossil insects. The scans usually have a fairly wide range of intensities depending on the specimen involved - for example, specimens in different types of amber can have vastly different intensity ranges, so I spend a lot of time tweaking intensity ranges and using Sphere brush with editable intensity ranges for different segments.

I was wondering if there is a way to save the intensity range last used for a given segment. Thus far I’ve resorted to just manually noting the intensity range used in the name of a segment, such as “Thorax muscle - 28.2k-max” or “Abdomen cuticle 14.4k-22.7k”. It would be a useful time saver to be able to switch to a segment and have it remember the editable intensity range last used for that segment.

If this doesn’t exist, I was considering looking into adding it. I have a software engineering/programming background and I’m happy to learn enough to be able to add this, but I wanted to make sure this didn’t already exist buried somewhere, or that someone else wasn’t already working on something like this.

Thanks in advance!

-Hollister


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http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ

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Re: Save editable intensity range for segments?

Hollister Herhold
In reply to this post by Hollister Herhold
I will give this a try.

Thanks for your help with my novice-level questions!!!

-Hollister



On Apr 6, 2017, at 10:55 AM, Andras Lasso <[hidden email]> wrote:

This is exactly what masking options in the Segment Editor is developed for.

 

The idea is that you create a “mask segment” for each tissue type with the threshold effect. The mask is a regular segment, that you select in the masking section as editable region (you'll be able to paint only inside the mask). Make sure disable overwriting segments (or hide the mask segment and choose to overwrite only visible segments).

 

I would also strongly suggest to try “grow from seeds” effect, as it makes segmentation incredibly fast and easy if you have enough intensity difference between your segments.

 

Use the latest nightly build of Slicer, as it contains many fixes and improvements compared to the latest stable version.

 

Andras

 

From: [hidden email]
Sent: Thursday, April 6, 2017 10:43 AM
To: [hidden email]
Subject: [slicer-devel] Save editable intensity range for segments?

 

Hi,

I’m a relatively new Slicer user (6 months or so), using Slicer to segment micro-CT scans of fossil insects. The scans usually have a fairly wide range of intensities depending on the specimen involved - for example, specimens in different types of amber can have vastly different intensity ranges, so I spend a lot of time tweaking intensity ranges and using Sphere brush with editable intensity ranges for different segments.

I was wondering if there is a way to save the intensity range last used for a given segment. Thus far I’ve resorted to just manually noting the intensity range used in the name of a segment, such as “Thorax muscle - 28.2k-max” or “Abdomen cuticle 14.4k-22.7k”. It would be a useful time saver to be able to switch to a segment and have it remember the editable intensity range last used for that segment.

If this doesn’t exist, I was considering looking into adding it. I have a software engineering/programming background and I’m happy to learn enough to be able to add this, but I wanted to make sure this didn’t already exist buried somewhere, or that someone else wasn’t already working on something like this.

Thanks in advance!

-Hollister


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ


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