TIFF to STL

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TIFF to STL

louiswolf
Hi,

Today I've started using Slicer, but after attempting to create a STL file (which I need for 3D printing) the entire day without any result, I've decided to try my luck here. I'm positively sure that what I'm trying to do should be possible, but apparently I won't be able to get there by myself.
I've been following the tutorials on The Open Source Paleontologist, and although they are somewhat outdated, they've been very useful in getting started. I've also looked at the training PDF's, but they don't seem to be very helpful in what I'm trying to achieve.

I get stuck at generating a Model. The interface tells me it's "Finished with errors" and that's about it. Both the Model Maker and the Grayscale Model Maker (the entire program crashes at 85% for the last one) aren't able to finish.

Here's are descriptions of what I do:
A
1 So, I've got black and white TIFF stack I'm importing
2 After opening the file I use "Volumes" to set the Image Spacing to 10
3 In "Models" I insert a hierargy
4 Then, through the "Editor" (I apply the GenericAnatomyColors), I apply the tissue label with ThresholdEffect
5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 1
6 I apply the parameters and get a "CompletedWithErrors" status message.
(6a. additionally, if I then close the scene now, the program crashes)
7 Nothing shows up in the 3D viewer and I don't get the option to save my volume as STL file in the Save Data dialog.

B
1 - 3 as described under A
4 I don't apply a label with ThresholdEffect
5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 0
6 The Model Maker finished without error (status message "Completed")
7 Nothing shows up in the 3D viewer. Also, I don't get the option to save my volume as STL file in the Save Data dialog.
(7a. additionally, if I go back to the editor and try to apply the tissue label anyway, the program crashes)

I can get a nice 3D image to show up with "Volume Rendering", but I don't think this is my model, right?

Can anyone give me some pointers in how to achieve my goal? It'll be a couple of days before I can reply again, but in the mean time, thanks for your help!
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Re: TIFF to STL

Kikinis, Ron,M.D.
http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Training#Slicer4_Neurosurgical_Planning_Tutorial

Once you have a labelmap in the editor, you should be able to use the
make model effect in the editor directly. See attached. The icon is in
the bottom row of effects on the right. Hit apply after selecting the
proper label value

When you set the image spacing in the volumes module, can you also set
the image origin to zero? In the 3d viewer, one of the icons in the
controller allows you to set the FOV of the camera. Icon in the top row
on the left.
http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/MainApplicationGUI#3D_Viewer

Finally, the pulldown called view gives you access to the errorlog,
where you can look at the error.

In order to create a stl file, select that format for the model when saving.


On 6/5/12 1:05 PM, louiswolf wrote:

> Hi,
>
> Today I've started using Slicer, but after attempting to create a STL file
> (which I need for 3D printing) the entire day without any result, I've
> decided to try my luck here. I'm positively sure that what I'm trying to do
> should be possible, but apparently I won't be able to get there by myself.
> I've been following the tutorials on
> http://openpaleo.blogspot.nl/2009/03/3d-slicer-tutorial-part-vi.html The
> Open Source Paleontologist , and although they are somewhat outdated,
> they've been very useful in getting started. I've also looked at the
> training PDF's, but they don't seem to be very helpful in what I'm trying to
> achieve.
>
> I get stuck at generating a Model. The interface tells me it's "Finished
> with errors" and that's about it. Both the Model Maker and the Grayscale
> Model Maker (the entire program crashes at 85% for the last one) aren't able
> to finish.
>
> Here's are descriptions of what I do:
> A
> 1 So, I've got black and white TIFF stack I'm importing
> 2 After opening the file I use "Volumes" to set the Image Spacing to 10
> 3 In "Models" I insert a hierargy
> 4 Then, through the "Editor" (I apply the GenericAnatomyColors), I apply the
> tissue label with ThresholdEffect
> 5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 1
> 6 I apply the parameters and get a "CompletedWithErrors" status message.
> (6a. additionally, if I then close the scene now, the program crashes)
> 7 Nothing shows up in the 3D viewer and I don't get the option to save my
> volume as STL file in the Save Data dialog.
>
> B
> 1 - 3 as described under A
> 4 I don't apply a label with ThresholdEffect
> 5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 0
> 6 The Model Maker finished without error (status message "Completed")
> 7 Nothing shows up in the 3D viewer. Also, I don't get the option to save my
> volume as STL file in the Save Data dialog.
> (7a. additionally, if I go back to the editor and try to apply the tissue
> label anyway, the program crashes)
>
> I can get a nice 3D image to show up with "Volume Rendering", but I don't
> think this is my model, right?
>
> Can anyone give me some pointers in how to achieve my goal? It'll be a
> couple of days before I can reply again, but in the mean time, thanks for
> your help!
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/TIFF-to-STL-tp4025066.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> 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
--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis

_______________________________________________
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: TIFF to STL

Kikinis, Ron,M.D.


On 6/5/12 1:20 PM, Ron Kikinis wrote:

> http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Training#Slicer4_Neurosurgical_Planning_Tutorial
>
>
> Once you have a labelmap in the editor, you should be able to use the
> make model effect in the editor directly. See attached. The icon is in
> the bottom row of effects on the right. Hit apply after selecting the
> proper label value
>
> When you set the image spacing in the volumes module, can you also set
> the image origin to zero? In the 3d viewer, one of the icons in the
> controller allows you to set the FOV of the camera. Icon in the top row
> on the left.
> http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/MainApplicationGUI#3D_Viewer
>
>
> Finally, the pulldown called view gives you access to the errorlog,
> where you can look at the error.
>
> In order to create a stl file, select that format for the model when
> saving.
>
>
> On 6/5/12 1:05 PM, louiswolf wrote:
>> Hi,
>>
>> Today I've started using Slicer, but after attempting to create a STL
>> file
>> (which I need for 3D printing) the entire day without any result, I've
>> decided to try my luck here. I'm positively sure that what I'm trying
>> to do
>> should be possible, but apparently I won't be able to get there by
>> myself.
>> I've been following the tutorials on
>> http://openpaleo.blogspot.nl/2009/03/3d-slicer-tutorial-part-vi.html The
>> Open Source Paleontologist , and although they are somewhat outdated,
>> they've been very useful in getting started. I've also looked at the
>> training PDF's, but they don't seem to be very helpful in what I'm
>> trying to
>> achieve.
>>
>> I get stuck at generating a Model. The interface tells me it's "Finished
>> with errors" and that's about it. Both the Model Maker and the Grayscale
>> Model Maker (the entire program crashes at 85% for the last one)
>> aren't able
>> to finish.
>>
>> Here's are descriptions of what I do:
>> A
>> 1 So, I've got black and white TIFF stack I'm importing
>> 2 After opening the file I use "Volumes" to set the Image Spacing to 10
>> 3 In "Models" I insert a hierargy
>> 4 Then, through the "Editor" (I apply the GenericAnatomyColors), I
>> apply the
>> tissue label with ThresholdEffect
>> 5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 1
>> 6 I apply the parameters and get a "CompletedWithErrors" status message.
>> (6a. additionally, if I then close the scene now, the program crashes)
>> 7 Nothing shows up in the 3D viewer and I don't get the option to save my
>> volume as STL file in the Save Data dialog.
>>
>> B
>> 1 - 3 as described under A
>> 4 I don't apply a label with ThresholdEffect
>> 5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 0
>> 6 The Model Maker finished without error (status message "Completed")
>> 7 Nothing shows up in the 3D viewer. Also, I don't get the option to
>> save my
>> volume as STL file in the Save Data dialog.
>> (7a. additionally, if I go back to the editor and try to apply the tissue
>> label anyway, the program crashes)
>>
>> I can get a nice 3D image to show up with "Volume Rendering", but I don't
>> think this is my model, right?
>>
>> Can anyone give me some pointers in how to achieve my goal? It'll be a
>> couple of days before I can reply again, but in the mean time, thanks for
>> your help!
>>
>>
>> --
>> View this message in context:
>> http://slicer-users.65878.n3.nabble.com/TIFF-to-STL-tp4025066.html
>> Sent from the slicer-users mailing list archive at Nabble.com.
>> _______________________________________________
>> 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
>
>
>
> _______________________________________________
> 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
--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis

_______________________________________________
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: TIFF to STL

Andras Lasso
In reply to this post by louiswolf
Maybe you have run out of memory. Start Slicer and enable the "Prefer
Executable CLIs" option in Edit / Application settings  / Modules. If the
model maker completes with errors then let us know what you see in the Error
Log (View / Error Log).

Andras

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of louiswolf
Sent: Tuesday, June 05, 2012 1:06 PM
To: [hidden email]
Subject: [slicer-users] TIFF to STL

Hi,

Today I've started using Slicer, but after attempting to create a STL file
(which I need for 3D printing) the entire day without any result, I've
decided to try my luck here. I'm positively sure that what I'm trying to do
should be possible, but apparently I won't be able to get there by myself.
I've been following the tutorials on
http://openpaleo.blogspot.nl/2009/03/3d-slicer-tutorial-part-vi.html The
Open Source Paleontologist , and although they are somewhat outdated,
they've been very useful in getting started. I've also looked at the
training PDF's, but they don't seem to be very helpful in what I'm trying to
achieve.

I get stuck at generating a Model. The interface tells me it's "Finished
with errors" and that's about it. Both the Model Maker and the Grayscale
Model Maker (the entire program crashes at 85% for the last one) aren't able
to finish.

Here's are descriptions of what I do:
A
1 So, I've got black and white TIFF stack I'm importing
2 After opening the file I use "Volumes" to set the Image Spacing to 10
3 In "Models" I insert a hierargy
4 Then, through the "Editor" (I apply the GenericAnatomyColors), I apply the
tissue label with ThresholdEffect
5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 1
6 I apply the parameters and get a "CompletedWithErrors" status message.
(6a. additionally, if I then close the scene now, the program crashes)
7 Nothing shows up in the 3D viewer and I don't get the option to save my
volume as STL file in the Save Data dialog.

B
1 - 3 as described under A
4 I don't apply a label with ThresholdEffect
5 Via the MakeModelEffect, I go to the Model Maker and set my Label to 0
6 The Model Maker finished without error (status message "Completed")
7 Nothing shows up in the 3D viewer. Also, I don't get the option to save my
volume as STL file in the Save Data dialog.
(7a. additionally, if I go back to the editor and try to apply the tissue
label anyway, the program crashes)

I can get a nice 3D image to show up with "Volume Rendering", but I don't
think this is my model, right?

Can anyone give me some pointers in how to achieve my goal? It'll be a
couple of days before I can reply again, but in the mean time, thanks for
your help!


--
View this message in context:
http://slicer-users.65878.n3.nabble.com/TIFF-to-STL-tp4025066.html
Sent from the slicer-users mailing list archive at Nabble.com.
_______________________________________________
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: TIFF to STL

louiswolf
In reply to this post by Kikinis, Ron,M.D.
Thank you for your help! I was able to create the required STL file with the pointers from Ron! I'll file some bug reports on the crashes btw.
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Re: TIFF to STL

karanm
This post has NOT been accepted by the mailing list yet.
In reply to this post by louiswolf
Hi,

I am trying to make a 3d model of a dental cbct images. Firstly i had difficuty loading .dcm files. It would open but show only axial cuts. Somehow i managed to change those files into .tiff using image J.

Now it shows all the views but in 3d viewer the images are out of the box. i tried to follow your steps to create a 3d model. At 2nd step on changing the image spacing to 10, the red green yellow windows go black.
If i proceed without that , on 4rd step in Editor, it does not detect the master volume only which is loaded. Thus i am not able to change the label!

Please help..
I am new to all this.. let me know if any tutorials i need to go through  

Thanks
Karan

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Re: TIFF to STL

arumiat
Hi Karan

this is an excellent tutorial that should take you through from start to finish.
https://www.youtube.com/watch?v=MKLWzD0PiIc

Have a watch and try, and if you still have questions be sure to post back. I'd start a new thread.
T
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Re: TIFF to STL

karanm
arumiat wrote
Hi Karan

this is an excellent tutorial that should take you through from start to finish.
https://www.youtube.com/watch?v=MKLWzD0PiIc

Have a watch and try, and if you still have questions be sure to post back. I'd start a new thread.
T
Hi Arumiat,

Thanks a ton for  such an immediate response. That tutorial simplified a lot of things and helped a lot!!! Have been trying all possible scans I have. On doing so I got a problem with loading CS 3D CBCT scans as it is. Error comes ' Can't Load Scalar Volume..' When I export those scan into CT images, Dicom dir and reduce the slice to 1mm then only it loads,otherwise doesn't. The machine can give slice thichness or voxels upto 90 microns. I have a lot of scans like that.

With that I loose the quality and details when preparing 3D model. Any way around it...??

Also I would like to know other ways for segmentation, especially for soft tissues. By threshold changes all soft tissues becomes one and connected!

Thanks a lot again.

Karan

 
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Re: TIFF to STL

arumiat
Regarding soft tissue segmentation Steve created a terrific tool but it's currently only available in an old version of Slicer, check out this thread for more details and Steve's videos to see if you think it might be of use. I have a copy of it but no longer at that location so let me know if you want it.

As for other soft tissue segmentation ultimately if your grayscale values are very close it's never going to be an easy job using segmentation tools to separate structures. I've had the best luck trying to produce as good as possible segmentation using Slicer, and then taking the resultant model into a modelling or sculpting program for cleanup. Blender.org is a good place to start. Again it depends on what you're ultimately trying to do.

For teeth extraction you should also check out ITK-snap which has an in-built level set segmentation tool that makes teeth extraction a bit easier.
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Re: TIFF to STL

Strugari, Matthew SCA


Matthew Strugari
Medical Physics Student
Department of Medical Physics
Saskatchewan Cancer Agency
20 Campus Drive
Saskatoon, SK S7N 4H4
Phone: (306) 655-2443
Fax: (306) 655-2701
email: [hidden email]
________________________________________
From: Strugari, Matthew SCA
Sent: October 17, 2014 9:32 AM
To: arumiat
Subject: RE: [slicer-users] TIFF to STL

Hi Arumiat,

I am interested in obtaining a copy of Slicer3 with the ModelDrawEffect. I would like to try to perform a semi-automatic segmentation of the hippocampus. From the videos that I saw here: https://dl.dropboxusercontent.com/u/1686930/IMAT-2011-09-23/index.html, this is just what I am looking for. My OS is Ubuntu 14.04 LTS so if I could get a copy of Slicer 3 and ModelDraw for a linux 64-bit machine that would be greatly appreciated.

Thanks!
Matthew
________________________________________
From: [hidden email] [[hidden email]] on behalf of arumiat [[hidden email]]
Sent: October 17, 2014 6:09 AM
To: [hidden email]
Subject: Re: [slicer-users] TIFF to STL

Regarding soft tissue segmentation Steve created a terrific tool but it's
currently only available in an old version of Slicer, check out this thread
<http://slicer-users.65878.n3.nabble.com/3d-crop-volume-td4027397.html>
for more details and Steve's videos to see if you think it might be of use.
I have a copy of it but no longer at that location so let me know if you
want it.

As for other soft tissue segmentation ultimately if your grayscale values
are very close it's never going to be an easy job using segmentation tools
to separate structures. I've had the best luck trying to produce as good as
possible segmentation using Slicer, and then taking the resultant model into
a modelling or sculpting program for cleanup. Blender.org is a good place to
start. Again it depends on what you're ultimately trying to do.

For teeth extraction you should also check out ITK-snap which has an
in-built level set segmentation tool that makes teeth extraction a bit
easier.



--
View this message in context: http://slicer-users.65878.n3.nabble.com/TIFF-to-STL-tp4025066p4028237.html
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Re: TIFF to STL

arumiat
RAR sent via WeTransfer (282MB file!).
Definitely works on Windows build, I'm not sure if it will also work on Linux. Best person to contact is Steve Pieper to see if he has any other builds, or try running it with Wine?
Be great to hear how you get on and see some of the results.
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Re: TIFF to STL

Steve Pieper-2
Hi - 

I don't have a linux build of that tool available anymore, unfortunately.  There's been some discussion lately about updating a version for slicer4 so I hope that will work out for everyone.

-Steve

On Fri, Oct 17, 2014 at 12:55 PM, arumiat <[hidden email]> wrote:
RAR sent via WeTransfer (282MB file!).
Definitely works on Windows build, I'm not sure if it will also work on
Linux. Best person to contact is Steve Pieper to see if he has any other
builds, or try running it with Wine?
Be great to hear how you get on and see some of the results.




--
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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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
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