Help

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

Help

Emmet Aylward
I have a DVD with 1331 Dicom images, I loaded these files to 3D Slicer , which obviously took quite since time to download but it did finish and I clicked OK .
My issue now is where did they go and how do I send those STL files to my contact .
Thank You for your time
Emmet

--

*Emmet *




_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Help

Steve Pieper-2
Hi Emmet - 

I'd suggest copying the data onto your hard disk first and not importing from DVD.

You'll find some tutorials on working with DICOM here:


And there are tutorials about 3D printing here:


And this video could be helpful:


You should be aware that converting dicom to stl is not a trivial process in general.

-Steve


On Tue, Feb 7, 2017 at 11:48 AM, Emmet Aylward <[hidden email]> wrote:
I have a DVD with 1331 Dicom images, I loaded these files to 3D Slicer , which obviously took quite since time to download but it did finish and I clicked OK .
My issue now is where did they go and how do I send those STL files to my contact .
Thank You for your time
Emmet

--

*Emmet *




_______________________________________________
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


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Help

Lars Grant-West

On Feb 7, 2017, at 3:02 PM, Steve Pieper <[hidden email]> wrote:

You should be aware that converting dicom to stl is not a trivial process in general

I second that emphatically. Internal voids, especially in bone - can be extremely problematic because they can create very thin walled structures when you go to print.

I’ve been loading the individual files into a single file, then opening in Photoshop. I created a minimally painful process to go through and fill internal voids. It’s easy when shapes are isolated, but any internal void which connects to the external surface (through any kind of hole passage in the bone) is, in 3D terms, a part of the external surface and.thus has to be manually disconnected.

I’m not conversant enough with 3D Slicer to manually draw out those passages in the 3D slicer windows, but it makes it very easy to figure out which holes are actually problematic.

Those internal voids which are themselves are not part of the external mesh are easy to remove in Blender, which is the 3D software I’m using.

Lars


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Help

Steve Pieper-2
In reply to this post by Steve Pieper-2
Also if your main goal is 3d printing of medical images the blogs and forums here might help: https://www.embodi3d.com/

Best of luck,
Steve

On Tue, Feb 7, 2017 at 3:31 PM, Lars Grant-West <[hidden email]> wrote:

On Feb 7, 2017, at 3:02 PM, Steve Pieper <[hidden email]> wrote:

You should be aware that converting dicom to stl is not a trivial process in general

I second that emphatically. Internal voids, especially in bone - can be extremely problematic because they can create very thin walled structures when you go to print.

I’ve been loading the individual files into a single file, then opening in Photoshop. I created a minimally painful process to go through and fill internal voids. It’s easy when shapes are isolated, but any internal void which connects to the external surface (through any kind of hole passage in the bone) is, in 3D terms, a part of the external surface and.thus has to be manually disconnected.

I’m not conversant enough with 3D Slicer to manually draw out those passages in the 3D slicer windows, but it makes it very easy to figure out which holes are actually problematic.

Those internal voids which are themselves are not part of the external mesh are easy to remove in Blender, which is the 3D software I’m using.

Lars



_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Help

Andras Lasso-2
In reply to this post by Lars Grant-West

You can use the segment editor to create solid bone models.

·         Small holes can be removed using Smoothing effect / Closing (fill holes) method.

·         Remaining larger holes can be filled by Islands effect / Add selected island method (click on the hole and it’ll be filled in 3D). Alternatively, you can create a new segment, add selected island outside the bone, and then invert the result (using Logical operators) – this removes all internal holes in one step.

·         If there are still holes then it means those holes are not fully enclosed in the bone segment. You can get rid of those using the Auto-complete effect / Grow from seeds method: Copy your bone segment to a new segment (using Logical operators), expand it by 5-10mm (using Margin effect), invert it (using Logical operators) – this will be your background segment. Running auto-complete / grow from seeds will fill the holes without leaking out from the bone. If there are areas where there is no contrast at all, then you have to manually modify the bone/background label using Paint effect.

 

Andras

 

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Lars Grant-West
Sent: February 7, 2017 15:31
To: Steve Pieper <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Help

 

 

On Feb 7, 2017, at 3:02 PM, Steve Pieper <[hidden email]> wrote:

 

You should be aware that converting dicom to stl is not a trivial process in general

 

I second that emphatically. Internal voids, especially in bone - can be extremely problematic because they can create very thin walled structures when you go to print.

 

I’ve been loading the individual files into a single file, then opening in Photoshop. I created a minimally painful process to go through and fill internal voids. It’s easy when shapes are isolated, but any internal void which connects to the external surface (through any kind of hole passage in the bone) is, in 3D terms, a part of the external surface and.thus has to be manually disconnected.

 

I’m not conversant enough with 3D Slicer to manually draw out those passages in the 3D slicer windows, but it makes it very easy to figure out which holes are actually problematic.

 

Those internal voids which are themselves are not part of the external mesh are easy to remove in Blender, which is the 3D software I’m using.

 

Lars

 


_______________________________________________
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
Reply | Threaded
Open this post in threaded view
|

Re: Help

Lars Grant-West
In reply to this post by Lars Grant-West
I’m just going to throw this out there -

This software has the most responsive technical help I’ve ever seen anywhere with anything.


On Feb 7, 2017, at 4:13 PM, Andras Lasso <[hidden email]> wrote:

You can use the segment editor to create solid bone models.
·         Small holes can be removed using Smoothing effect / Closing (fill holes) method.
·         Remaining larger holes can be filled by Islands effect / Add selected island method (click on the hole and it’ll be filled in 3D). Alternatively, you can create a new segment, add selected island outside the bone, and then invert the result (using Logical operators) – this removes all internal holes in one step.
·         If there are still holes then it means those holes are not fully enclosed in the bone segment. You can get rid of those using the Auto-complete effect / Grow from seeds method: Copy your bone segment to a new segment (using Logical operators), expand it by 5-10mm (using Margin effect), invert it (using Logical operators) – this will be your background segment. Running auto-complete / grow from seeds will fill the holes without leaking out from the bone. If there are areas where there is no contrast at all, then you have to manually modify the bone/background label using Paint effect.
 
Andras
 
 
From: slicer-users [[hidden email]] On Behalf Of Lars Grant-West
Sent: February 7, 2017 15:31
To: Steve Pieper <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Help
 
 
On Feb 7, 2017, at 3:02 PM, Steve Pieper <[hidden email]> wrote:
 
You should be aware that converting dicom to stl is not a trivial process in general
 
I second that emphatically. Internal voids, especially in bone - can be extremely problematic because they can create very thin walled structures when you go to print.
 
I’ve been loading the individual files into a single file, then opening in Photoshop. I created a minimally painful process to go through and fill internal voids. It’s easy when shapes are isolated, but any internal void which connects to the external surface (through any kind of hole passage in the bone) is, in 3D terms, a part of the external surface and.thus has to be manually disconnected.
 
I’m not conversant enough with 3D Slicer to manually draw out those passages in the 3D slicer windows, but it makes it very easy to figure out which holes are actually problematic.
 
Those internal voids which are themselves are not part of the external mesh are easy to remove in Blender, which is the 3D software I’m using.
 
Lars


_______________________________________________
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