Slicer texture analysis and radiomics

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Slicer texture analysis and radiomics

Greg Tarr
Hi - I'm wanting to use Slicer and automatically segment haematomas on CT
scans, then use radiomics and texture analysis to see if these features
predict outcomes.
I'm getting pretty good automatic segmentation, and now I'm looking for an
open source program which will allow me to extract texture and radiomics
features from the 3D volumes.

Does anyone have experience in this?

Cheers,
Greg



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Re: Slicer texture analysis and radiomics

Andrey Fedorov-2
https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/HeterogeneityCAD

On Fri, Mar 11, 2016 at 12:07 AM, Greg Tarr <[hidden email]> wrote:
Hi - I'm wanting to use Slicer and automatically segment haematomas on CT
scans, then use radiomics and texture analysis to see if these features
predict outcomes.
I'm getting pretty good automatic segmentation, and now I'm looking for an
open source program which will allow me to extract texture and radiomics
features from the 3D volumes.

Does anyone have experience in this?

Cheers,
Greg



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Re: Slicer texture analysis and radiomics

bpaniagua
Hello Greg,



I believe that Raul SJ in BWH - Harvard has developed an extension called
ChestImagingPlatform for Slicer that does some ROI texture analysis in
pulmonary CTs.

More info:
https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly#Modules_by_category_Chest_Imaging_Platform


My team has worked on some code to do texture analysis to analyze CBCT bone
texture. We do not have this deployed as a Slicer extension, but I you can
find the research code here https://github.com/NIRALUser/TextureRLE.


HTH,
Beatriz





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Re: Slicer texture analysis and radiomics

bpaniagua
This post has NOT been accepted by the mailing list yet.
In reply to this post by Andrey Fedorov-2
Hello Greg,



I believe that Raul SJ in BWH - Harvard has developed an extension called ChestImagingPlatform for Slicer that does some ROI texture analysis in pulmonary CTs.

More info: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly#Modules_by_category_Chest_Imaging_Platform


My team has worked on some code to do texture analysis to analyze CBCT bone texture. We do not have this deployed as a Slicer extension, but I you can find the research code here https://github.com/NIRALUser/TextureRLE.


HTH,
Beatriz

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Re: Slicer texture analysis and radiomics

Greg Tarr
In reply to this post by bpaniagua
Cool - thanks for they help everyone.

I am trying out the CAD Heterogeneity module and I have two thoughts.

Firstly, is there any way to make this faster? I'm analysing haemorrhages ranging from 1/2 mL up to 300 mL, and while the smaller ones are quick, it looks like one measuring >150 mL will take hours... I'm not sure how many hours yet.

Secondly, is there an easy way to automate the texture analysis? Say I segment them all, saving the ROI map for each scan into a seperate folder (with the original scan), can I set it up so that it will sequentially analyse all of the textures and then save the outputs?

Cheers,
Greg
________________________________________
From: [hidden email] <[hidden email]> on behalf of bpaniagua <[hidden email]>
Sent: Saturday, March 12, 2016 3:34 AM
To: SPL Slicer Users
Subject: Re: [slicer-users] Slicer texture analysis and radiomics

Hello Greg,



I believe that Raul SJ in BWH - Harvard has developed an extension called
ChestImagingPlatform for Slicer that does some ROI texture analysis in
pulmonary CTs.

More info:
https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly#Modules_by_category_Chest_Imaging_Platform


My team has worked on some code to do texture analysis to analyze CBCT bone
texture. We do not have this deployed as a Slicer extension, but I you can
find the research code here https://github.com/NIRALUser/TextureRLE.


HTH,
Beatriz





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Re: Slicer texture analysis and radiomics

Andrey Fedorov-2
Greg, 

Jay cc'd is the lead of that extension and should have the answers.

AF

On Sun, Mar 13, 2016, 04:14 Gregory Tarr <[hidden email]> wrote:
Cool - thanks for they help everyone.

I am trying out the CAD Heterogeneity module and I have two thoughts.

Firstly, is there any way to make this faster? I'm analysing haemorrhages ranging from 1/2 mL up to 300 mL, and while the smaller ones are quick, it looks like one measuring >150 mL will take hours... I'm not sure how many hours yet.

Secondly, is there an easy way to automate the texture analysis? Say I segment them all, saving the ROI map for each scan into a seperate folder (with the original scan), can I set it up so that it will sequentially analyse all of the textures and then save the outputs?

Cheers,
Greg
________________________________________
From: [hidden email] <[hidden email]> on behalf of bpaniagua <[hidden email]>
Sent: Saturday, March 12, 2016 3:34 AM
To: SPL Slicer Users
Subject: Re: [slicer-users] Slicer texture analysis and radiomics

Hello Greg,



I believe that Raul SJ in BWH - Harvard has developed an extension called
ChestImagingPlatform for Slicer that does some ROI texture analysis in
pulmonary CTs.

More info:
https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly#Modules_by_category_Chest_Imaging_Platform


My team has worked on some code to do texture analysis to analyze CBCT bone
texture. We do not have this deployed as a Slicer extension, but I you can
find the research code here https://github.com/NIRALUser/TextureRLE.


HTH,
Beatriz





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