CT Mummy Scan - Segmenting bone

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

CT Mummy Scan - Segmenting bone

Louise vdw
Hello All, 

I have a CT scan of a Mummy and am looking to segment the bone to create a skull model for 3D printing. Normally this would be quite straightforward but the specimen is obviously very old and quite degraded. The contrast between the bone and surrounding dessicated tissue/fabric is not very good. The bones are effectively hollow and look patchy in places. 

I am currently trying to segment using the Threshold function under the Editor module, with manual clean up afterwards using tools like SaveIsland, Paint,  etc, but it is extremely laborious.
I have attached a screenshot of the dataset as well as one of the models I have generated.  I end up with a lot of holes in the skull if I set the threshold to exclude surrounding tissue, but if I set the threshold higher there is a lot of excess tissue to clean afterwards. 

My question, is there any better way to do this? or are there any image filters I could pass the data through to clean it up prior to segmentation?

I assume I will have to pass the model through a postprocessing package such as MeshMixer or NetFabb to clean it up further, but the more I can do in Slicer, the better. 

Thanks in advance!

Regards, 
Louise van der Werff

_______________________________________________
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.

Mummy CT.jpg (71K) Download Attachment
Mummy CT model.jpg (99K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: CT Mummy Scan - Segmenting bone

Andras Lasso-2

If only a few then the fastest is still to use semi-automatic methods:

·         Threshold

·         Apply binary filters in Simple Filters module (BinaryFillholeImageFilter, etc.)

·         Erase large areas using Volume clip with model extension

·         Erase smaller areas by painting with sphere brush

and then go through each slice and fix them manually using paint and draw). You make the process much faster by resampling the original CT at a coarser grid – at the cost of losing some small details.

 

If you have tens or hundreds of these volumes to segment then you may consider developing an optimized, more automated workflow but for a couple of volumes it is still much faster to do a lot of manual work.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Louise van der Werff
Sent: Thursday, September 10, 2015 12:33 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] CT Mummy Scan - Segmenting bone

 

Hello All, 

 

I have a CT scan of a Mummy and am looking to segment the bone to create a skull model for 3D printing. Normally this would be quite straightforward but the specimen is obviously very old and quite degraded. The contrast between the bone and surrounding dessicated tissue/fabric is not very good. The bones are effectively hollow and look patchy in places. 

 

I am currently trying to segment using the Threshold function under the Editor module, with manual clean up afterwards using tools like SaveIsland, Paint,  etc, but it is extremely laborious.

I have attached a screenshot of the dataset as well as one of the models I have generated.  I end up with a lot of holes in the skull if I set the threshold to exclude surrounding tissue, but if I set the threshold higher there is a lot of excess tissue to clean afterwards. 

 

My question, is there any better way to do this? or are there any image filters I could pass the data through to clean it up prior to segmentation?

 

I assume I will have to pass the model through a postprocessing package such as MeshMixer or NetFabb to clean it up further, but the more I can do in Slicer, the better. 

 

Thanks in advance!

 

Regards, 

Louise van der Werff


_______________________________________________
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.
Reply | Threaded
Open this post in threaded view
|

Re: CT Mummy Scan - Segmenting bone

Tamas Ungi-2

I did some similar jobs for creating training models from patient data. I had CT images of live people, and still spent several hours manually going through every slice to add or erase labels. I think if you want a really nice model in the end, that is the only way to go.

 

When you are done editing manually, don't forget to apply some smoothing on your labelmap (e.g. by dilate and erode), or on the generated surface model. So marks of slice-by-slice manual editing don't show up on the final model.

 

Tamas

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Andras Lasso
Sent: September 10, 2015 3:19 PM
To: Louise van der Werff <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] CT Mummy Scan - Segmenting bone

 

If only a few then the fastest is still to use semi-automatic methods:

·         Threshold

·         Apply binary filters in Simple Filters module (BinaryFillholeImageFilter, etc.)

·         Erase large areas using Volume clip with model extension

·         Erase smaller areas by painting with sphere brush

and then go through each slice and fix them manually using paint and draw). You make the process much faster by resampling the original CT at a coarser grid – at the cost of losing some small details.

 

If you have tens or hundreds of these volumes to segment then you may consider developing an optimized, more automated workflow but for a couple of volumes it is still much faster to do a lot of manual work.

 

Andras

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Louise van der Werff
Sent: Thursday, September 10, 2015 12:33 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] CT Mummy Scan - Segmenting bone

 

Hello All, 

 

I have a CT scan of a Mummy and am looking to segment the bone to create a skull model for 3D printing. Normally this would be quite straightforward but the specimen is obviously very old and quite degraded. The contrast between the bone and surrounding dessicated tissue/fabric is not very good. The bones are effectively hollow and look patchy in places. 

 

I am currently trying to segment using the Threshold function under the Editor module, with manual clean up afterwards using tools like SaveIsland, Paint,  etc, but it is extremely laborious.

I have attached a screenshot of the dataset as well as one of the models I have generated.  I end up with a lot of holes in the skull if I set the threshold to exclude surrounding tissue, but if I set the threshold higher there is a lot of excess tissue to clean afterwards. 

 

My question, is there any better way to do this? or are there any image filters I could pass the data through to clean it up prior to segmentation?

 

I assume I will have to pass the model through a postprocessing package such as MeshMixer or NetFabb to clean it up further, but the more I can do in Slicer, the better. 

 

Thanks in advance!

 

Regards, 

Louise van der Werff


_______________________________________________
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.