Need help with application

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Need help with application

Jan Allbright
Hello all,

I am a Vietnam veteran with a TBI.
I recently got a CT scan of the head and received a copy of the images,
which I have successfully viewed via "Reviewer".
I got the idea of using Slicer to generate a mesh that I could feed to a
3D printer so that I could have a model of my damaged brain, but Slicer
is not co-operating.
I load up the coronal view (DICOM), and it shows up in the three views,
but the 3d rendering does not appear to function and since I don't see
any error messages I am at a loss as to how to proceed.

Any help from anyone would be greatly appreciated.

- Jan Allbright
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Re: Need help with application

Aucoin, Nicole
Hello Jan,

There¹s a video tutorial available that should be helpful:
https://www.youtube.com/watch?v=MKLWzD0PiIc

Nicole

On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:

>Hello all,
>
>I am a Vietnam veteran with a TBI.
>I recently got a CT scan of the head and received a copy of the images,
>which I have successfully viewed via "Reviewer".
>I got the idea of using Slicer to generate a mesh that I could feed to a
>3D printer so that I could have a model of my damaged brain, but Slicer
>is not co-operating.
>I load up the coronal view (DICOM), and it shows up in the three views,
>but the 3d rendering does not appear to function and since I don't see
>any error messages I am at a loss as to how to proceed.
>
>Any help from anyone would be greatly appreciated.
>
>- Jan Allbright
>_______________________________________________
>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

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Re: Need help with application

Andrey Fedorov-2
Jan,

As a general comment, CT is not the optimal modality for visualizing
brain soft tissue. If you have an MR scan, it would be more suitable
for this task.

Were you looking to just segment the cortical surface, or something else?

Let us know about your experience learning from the tutorial.

AF

On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole <[hidden email]> wrote:

> Hello Jan,
>
> There¹s a video tutorial available that should be helpful:
> https://www.youtube.com/watch?v=MKLWzD0PiIc
>
> Nicole
>
> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>
>>Hello all,
>>
>>I am a Vietnam veteran with a TBI.
>>I recently got a CT scan of the head and received a copy of the images,
>>which I have successfully viewed via "Reviewer".
>>I got the idea of using Slicer to generate a mesh that I could feed to a
>>3D printer so that I could have a model of my damaged brain, but Slicer
>>is not co-operating.
>>I load up the coronal view (DICOM), and it shows up in the three views,
>>but the 3d rendering does not appear to function and since I don't see
>>any error messages I am at a loss as to how to proceed.
>>
>>Any help from anyone would be greatly appreciated.
>>
>>- Jan Allbright
>>_______________________________________________
>>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
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Re: Need help with application

Jan Allbright
In reply to this post by Aucoin, Nicole
I have followed the steps laid out in many "how-to" pages and also
followed the video.
At 10 minutes the demonstrator invokes the Volume Render and the head
appears in the 3D window.
In my case nothing happens .. no spinner, no error message, nothing.
The other three windows function as advertised including brightness and
contrast functions.
ITK-SNAP pretty much responds the same way.
I am thinking there must be something wrong with my data-set, but my
understanding of DICOM data is very superficial.
Is it possible that the data can be such that the standard views are OK
but are somehow corrupted as to prevent the 3D rendering?
This is from a Veterans Administration data-set. Could there be
something missing?

As to the choice of CT vs MRI, I have residual metallic fragments in my
scalp that prohibit the MRI.

Bone and Cortical imaging would be ideal but inasmuch as I currently
seeing zero, any advance would be great.

Again .. thanks in advance for all the time and effort!

- Jan Allbright

On 10/18/2016 07:36, Andrey Fedorov wrote:

> Jan,
>
> As a general comment, CT is not the optimal modality for visualizing
> brain soft tissue. If you have an MR scan, it would be more suitable
> for this task.
>
> Were you looking to just segment the cortical surface, or something else?
>
> Let us know about your experience learning from the tutorial.
>
> AF
>
> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole <[hidden email]> wrote:
>> Hello Jan,
>>
>> There¹s a video tutorial available that should be helpful:
>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>
>> Nicole
>>
>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>
>>> Hello all,
>>>
>>> I am a Vietnam veteran with a TBI.
>>> I recently got a CT scan of the head and received a copy of the images,
>>> which I have successfully viewed via "Reviewer".
>>> I got the idea of using Slicer to generate a mesh that I could feed to a
>>> 3D printer so that I could have a model of my damaged brain, but Slicer
>>> is not co-operating.
>>> I load up the coronal view (DICOM), and it shows up in the three views,
>>> but the 3d rendering does not appear to function and since I don't see
>>> any error messages I am at a loss as to how to proceed.
>>>
>>> Any help from anyone would be greatly appreciated.
>>>
>>> - Jan Allbright
>>> _______________________________________________
>>> 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

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Re: Need help with application

Ramon F Herrera

Jan:

 Try the steps in the attached image.

-RFH

On Wed, Oct 19, 2016 at 01:14:41PM +0000, Jan Allbright wrote:

> I have followed the steps laid out in many "how-to" pages and also
> followed the video.
> At 10 minutes the demonstrator invokes the Volume Render and the head
> appears in the 3D window.
> In my case nothing happens .. no spinner, no error message, nothing.
> The other three windows function as advertised including brightness and
> contrast functions.
> ITK-SNAP pretty much responds the same way.
> I am thinking there must be something wrong with my data-set, but my
> understanding of DICOM data is very superficial.
> Is it possible that the data can be such that the standard views are OK
> but are somehow corrupted as to prevent the 3D rendering?
> This is from a Veterans Administration data-set. Could there be
> something missing?
>
> As to the choice of CT vs MRI, I have residual metallic fragments in my
> scalp that prohibit the MRI.
>
> Bone and Cortical imaging would be ideal but inasmuch as I currently
> seeing zero, any advance would be great.
>
> Again .. thanks in advance for all the time and effort!
>
> - Jan Allbright
>

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Re: Need help with application

Aucoin, Nicole
In reply to this post by Aucoin, Nicole
Hi Jan,

It sounds like an issue with your video card combined with the 3D volume
rendering method. If you click on the red X at the bottom right, it should
bring up an error log that might give you more information. You can also
go into the Volume Rendering Module, the Rendering drop down menu in the
Display section has a few options (assumign that the eye icon next to the
Volume selector showing MRHead is open). Try the different rendering modes
and see if that helps.
Also, which version of Slicer are you using? (Slicer->About)

Nicole

On 10/19/16, 9:14 AM, "Jan Allbright" <[hidden email]> wrote:

>I have followed the steps laid out in many "how-to" pages and also
>followed the video.
>At 10 minutes the demonstrator invokes the Volume Render and the head
>appears in the 3D window.
>In my case nothing happens .. no spinner, no error message, nothing.
>The other three windows function as advertised including brightness and
>contrast functions.
>ITK-SNAP pretty much responds the same way.
>I am thinking there must be something wrong with my data-set, but my
>understanding of DICOM data is very superficial.
>Is it possible that the data can be such that the standard views are OK
>but are somehow corrupted as to prevent the 3D rendering?
>This is from a Veterans Administration data-set. Could there be
>something missing?
>
>As to the choice of CT vs MRI, I have residual metallic fragments in my
>scalp that prohibit the MRI.
>
>Bone and Cortical imaging would be ideal but inasmuch as I currently
>seeing zero, any advance would be great.
>
>Again .. thanks in advance for all the time and effort!
>
>- Jan Allbright
>
>On 10/18/2016 07:36, Andrey Fedorov wrote:
>> Jan,
>>
>> As a general comment, CT is not the optimal modality for visualizing
>> brain soft tissue. If you have an MR scan, it would be more suitable
>> for this task.
>>
>> Were you looking to just segment the cortical surface, or something
>>else?
>>
>> Let us know about your experience learning from the tutorial.
>>
>> AF
>>
>> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole
>><[hidden email]> wrote:
>>> Hello Jan,
>>>
>>> There¹s a video tutorial available that should be helpful:
>>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>>
>>> Nicole
>>>
>>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>>
>>>> Hello all,
>>>>
>>>> I am a Vietnam veteran with a TBI.
>>>> I recently got a CT scan of the head and received a copy of the
>>>>images,
>>>> which I have successfully viewed via "Reviewer".
>>>> I got the idea of using Slicer to generate a mesh that I could feed
>>>>to a
>>>> 3D printer so that I could have a model of my damaged brain, but
>>>>Slicer
>>>> is not co-operating.
>>>> I load up the coronal view (DICOM), and it shows up in the three
>>>>views,
>>>> but the 3d rendering does not appear to function and since I don't see
>>>> any error messages I am at a loss as to how to proceed.
>>>>
>>>> Any help from anyone would be greatly appreciated.
>>>>
>>>> - Jan Allbright
>>>> _______________________________________________
>>>> 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
>

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Re: Need help with application

Aucoin, Nicole

Also: try out different Presets in the Display panel, there are some
transfer functions that are better for various CT scans.

Nicole

On 10/19/16, 10:02 AM, "Aucoin, Nicole" <[hidden email]> wrote:

>Hi Jan,
>
>It sounds like an issue with your video card combined with the 3D volume
>rendering method. If you click on the red X at the bottom right, it should
>bring up an error log that might give you more information. You can also
>go into the Volume Rendering Module, the Rendering drop down menu in the
>Display section has a few options (assumign that the eye icon next to the
>Volume selector showing MRHead is open). Try the different rendering modes
>and see if that helps.
>Also, which version of Slicer are you using? (Slicer->About)
>
>Nicole
>
>On 10/19/16, 9:14 AM, "Jan Allbright" <[hidden email]> wrote:
>
>>I have followed the steps laid out in many "how-to" pages and also
>>followed the video.
>>At 10 minutes the demonstrator invokes the Volume Render and the head
>>appears in the 3D window.
>>In my case nothing happens .. no spinner, no error message, nothing.
>>The other three windows function as advertised including brightness and
>>contrast functions.
>>ITK-SNAP pretty much responds the same way.
>>I am thinking there must be something wrong with my data-set, but my
>>understanding of DICOM data is very superficial.
>>Is it possible that the data can be such that the standard views are OK
>>but are somehow corrupted as to prevent the 3D rendering?
>>This is from a Veterans Administration data-set. Could there be
>>something missing?
>>
>>As to the choice of CT vs MRI, I have residual metallic fragments in my
>>scalp that prohibit the MRI.
>>
>>Bone and Cortical imaging would be ideal but inasmuch as I currently
>>seeing zero, any advance would be great.
>>
>>Again .. thanks in advance for all the time and effort!
>>
>>- Jan Allbright
>>
>>On 10/18/2016 07:36, Andrey Fedorov wrote:
>>> Jan,
>>>
>>> As a general comment, CT is not the optimal modality for visualizing
>>> brain soft tissue. If you have an MR scan, it would be more suitable
>>> for this task.
>>>
>>> Were you looking to just segment the cortical surface, or something
>>>else?
>>>
>>> Let us know about your experience learning from the tutorial.
>>>
>>> AF
>>>
>>> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole
>>><[hidden email]> wrote:
>>>> Hello Jan,
>>>>
>>>> There¹s a video tutorial available that should be helpful:
>>>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>>>
>>>> Nicole
>>>>
>>>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> I am a Vietnam veteran with a TBI.
>>>>> I recently got a CT scan of the head and received a copy of the
>>>>>images,
>>>>> which I have successfully viewed via "Reviewer".
>>>>> I got the idea of using Slicer to generate a mesh that I could feed
>>>>>to a
>>>>> 3D printer so that I could have a model of my damaged brain, but
>>>>>Slicer
>>>>> is not co-operating.
>>>>> I load up the coronal view (DICOM), and it shows up in the three
>>>>>views,
>>>>> but the 3d rendering does not appear to function and since I don't
>>>>>see
>>>>> any error messages I am at a loss as to how to proceed.
>>>>>
>>>>> Any help from anyone would be greatly appreciated.
>>>>>
>>>>> - Jan Allbright
>>>>> _______________________________________________
>>>>> 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
>>
>
>_______________________________________________
>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

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Re: Need help with application

inorton
In reply to this post by Jan Allbright
In my case nothing happens .. no spinner, no error message, nothing.
The other three windows function as advertised including brightness and
contrast functions.
ITK-SNAP pretty much responds the same way.
I am thinking there must be something wrong with my data-set, but my
understanding of DICOM data is very superficial.

Some suggestions to debug whether the issue is w/ your data or elsewhere:

- try one of the sample datasets (File menu -> Download Sample Data)
- try various different presets (first under the "Display" section in the Volume Rendering module)

If those don't work, the issue may be related to your graphics card.

Also, please check the error log and send: Help menu -> Report a Bug -> Copy error messages to clipboard.

Best,
Isaiah 

On Wed, Oct 19, 2016 at 9:14 AM, Jan Allbright <[hidden email]> wrote:
I have followed the steps laid out in many "how-to" pages and also
followed the video.
At 10 minutes the demonstrator invokes the Volume Render and the head
appears in the 3D window.
In my case nothing happens .. no spinner, no error message, nothing.
The other three windows function as advertised including brightness and
contrast functions.
ITK-SNAP pretty much responds the same way.
I am thinking there must be something wrong with my data-set, but my
understanding of DICOM data is very superficial.
Is it possible that the data can be such that the standard views are OK
but are somehow corrupted as to prevent the 3D rendering?
This is from a Veterans Administration data-set. Could there be
something missing?

As to the choice of CT vs MRI, I have residual metallic fragments in my
scalp that prohibit the MRI.

Bone and Cortical imaging would be ideal but inasmuch as I currently
seeing zero, any advance would be great.

Again .. thanks in advance for all the time and effort!

- Jan Allbright

On 10/18/2016 07:36, Andrey Fedorov wrote:
> Jan,
>
> As a general comment, CT is not the optimal modality for visualizing
> brain soft tissue. If you have an MR scan, it would be more suitable
> for this task.
>
> Were you looking to just segment the cortical surface, or something else?
>
> Let us know about your experience learning from the tutorial.
>
> AF
>
> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole <[hidden email]> wrote:
>> Hello Jan,
>>
>> There¹s a video tutorial available that should be helpful:
>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>
>> Nicole
>>
>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>
>>> Hello all,
>>>
>>> I am a Vietnam veteran with a TBI.
>>> I recently got a CT scan of the head and received a copy of the images,
>>> which I have successfully viewed via "Reviewer".
>>> I got the idea of using Slicer to generate a mesh that I could feed to a
>>> 3D printer so that I could have a model of my damaged brain, but Slicer
>>> is not co-operating.
>>> I load up the coronal view (DICOM), and it shows up in the three views,
>>> but the 3d rendering does not appear to function and since I don't see
>>> any error messages I am at a loss as to how to proceed.
>>>
>>> Any help from anyone would be greatly appreciated.
>>>
>>> - Jan Allbright
>>> _______________________________________________
>>> 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

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Re: Need help with application

Andrey Fedorov-2
In reply to this post by Aucoin, Nicole
Jan,

to get back to your original issue, if I understand it correctly -
"using Slicer to generate a mesh that I could feed to a 3D printer".

I recorded a quick screencast showing how to get 3d view of the kind
you want to see (if I understand it correctly):

http://www.screencast.com/t/I0TQS5Qcm (this is for MR, since I don't
have a sample head CT handy).

There are two parts - volume rendering, that can help you explore the
data, and surface extraction, which generates a triangulation that you
can save and potentially use for 3d printing.

As I was going over the demo, I realized that using Segment Editor
does not generate a surface that could be saved, so that is a caveat,
but hopefully this will help you a little bit to get going with your
data.

AF

On Wed, Oct 19, 2016 at 10:06 AM, Aucoin, Nicole <[hidden email]> wrote:

>
> Also: try out different Presets in the Display panel, there are some
> transfer functions that are better for various CT scans.
>
> Nicole
>
> On 10/19/16, 10:02 AM, "Aucoin, Nicole" <[hidden email]> wrote:
>
>>Hi Jan,
>>
>>It sounds like an issue with your video card combined with the 3D volume
>>rendering method. If you click on the red X at the bottom right, it should
>>bring up an error log that might give you more information. You can also
>>go into the Volume Rendering Module, the Rendering drop down menu in the
>>Display section has a few options (assumign that the eye icon next to the
>>Volume selector showing MRHead is open). Try the different rendering modes
>>and see if that helps.
>>Also, which version of Slicer are you using? (Slicer->About)
>>
>>Nicole
>>
>>On 10/19/16, 9:14 AM, "Jan Allbright" <[hidden email]> wrote:
>>
>>>I have followed the steps laid out in many "how-to" pages and also
>>>followed the video.
>>>At 10 minutes the demonstrator invokes the Volume Render and the head
>>>appears in the 3D window.
>>>In my case nothing happens .. no spinner, no error message, nothing.
>>>The other three windows function as advertised including brightness and
>>>contrast functions.
>>>ITK-SNAP pretty much responds the same way.
>>>I am thinking there must be something wrong with my data-set, but my
>>>understanding of DICOM data is very superficial.
>>>Is it possible that the data can be such that the standard views are OK
>>>but are somehow corrupted as to prevent the 3D rendering?
>>>This is from a Veterans Administration data-set. Could there be
>>>something missing?
>>>
>>>As to the choice of CT vs MRI, I have residual metallic fragments in my
>>>scalp that prohibit the MRI.
>>>
>>>Bone and Cortical imaging would be ideal but inasmuch as I currently
>>>seeing zero, any advance would be great.
>>>
>>>Again .. thanks in advance for all the time and effort!
>>>
>>>- Jan Allbright
>>>
>>>On 10/18/2016 07:36, Andrey Fedorov wrote:
>>>> Jan,
>>>>
>>>> As a general comment, CT is not the optimal modality for visualizing
>>>> brain soft tissue. If you have an MR scan, it would be more suitable
>>>> for this task.
>>>>
>>>> Were you looking to just segment the cortical surface, or something
>>>>else?
>>>>
>>>> Let us know about your experience learning from the tutorial.
>>>>
>>>> AF
>>>>
>>>> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole
>>>><[hidden email]> wrote:
>>>>> Hello Jan,
>>>>>
>>>>> There¹s a video tutorial available that should be helpful:
>>>>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>>>>
>>>>> Nicole
>>>>>
>>>>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I am a Vietnam veteran with a TBI.
>>>>>> I recently got a CT scan of the head and received a copy of the
>>>>>>images,
>>>>>> which I have successfully viewed via "Reviewer".
>>>>>> I got the idea of using Slicer to generate a mesh that I could feed
>>>>>>to a
>>>>>> 3D printer so that I could have a model of my damaged brain, but
>>>>>>Slicer
>>>>>> is not co-operating.
>>>>>> I load up the coronal view (DICOM), and it shows up in the three
>>>>>>views,
>>>>>> but the 3d rendering does not appear to function and since I don't
>>>>>>see
>>>>>> any error messages I am at a loss as to how to proceed.
>>>>>>
>>>>>> Any help from anyone would be greatly appreciated.
>>>>>>
>>>>>> - Jan Allbright
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>
>>_______________________________________________
>>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
>
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Re: Need help with application

Fernando Pérez-García
​@Andrey: you can generate the surface with the Segmentations module after you've edited your segmentation using the Segment Editor module.

Fernando​

2016-10-19 16:47 GMT+02:00 Andrey Fedorov <[hidden email]>:
Jan,

to get back to your original issue, if I understand it correctly -
"using Slicer to generate a mesh that I could feed to a 3D printer".

I recorded a quick screencast showing how to get 3d view of the kind
you want to see (if I understand it correctly):

http://www.screencast.com/t/I0TQS5Qcm (this is for MR, since I don't
have a sample head CT handy).

There are two parts - volume rendering, that can help you explore the
data, and surface extraction, which generates a triangulation that you
can save and potentially use for 3d printing.

As I was going over the demo, I realized that using Segment Editor
does not generate a surface that could be saved, so that is a caveat,
but hopefully this will help you a little bit to get going with your
data.

AF

On Wed, Oct 19, 2016 at 10:06 AM, Aucoin, Nicole <[hidden email]> wrote:
>
> Also: try out different Presets in the Display panel, there are some
> transfer functions that are better for various CT scans.
>
> Nicole
>
> On 10/19/16, 10:02 AM, "Aucoin, Nicole" <[hidden email]> wrote:
>
>>Hi Jan,
>>
>>It sounds like an issue with your video card combined with the 3D volume
>>rendering method. If you click on the red X at the bottom right, it should
>>bring up an error log that might give you more information. You can also
>>go into the Volume Rendering Module, the Rendering drop down menu in the
>>Display section has a few options (assumign that the eye icon next to the
>>Volume selector showing MRHead is open). Try the different rendering modes
>>and see if that helps.
>>Also, which version of Slicer are you using? (Slicer->About)
>>
>>Nicole
>>
>>On 10/19/16, 9:14 AM, "Jan Allbright" <[hidden email]> wrote:
>>
>>>I have followed the steps laid out in many "how-to" pages and also
>>>followed the video.
>>>At 10 minutes the demonstrator invokes the Volume Render and the head
>>>appears in the 3D window.
>>>In my case nothing happens .. no spinner, no error message, nothing.
>>>The other three windows function as advertised including brightness and
>>>contrast functions.
>>>ITK-SNAP pretty much responds the same way.
>>>I am thinking there must be something wrong with my data-set, but my
>>>understanding of DICOM data is very superficial.
>>>Is it possible that the data can be such that the standard views are OK
>>>but are somehow corrupted as to prevent the 3D rendering?
>>>This is from a Veterans Administration data-set. Could there be
>>>something missing?
>>>
>>>As to the choice of CT vs MRI, I have residual metallic fragments in my
>>>scalp that prohibit the MRI.
>>>
>>>Bone and Cortical imaging would be ideal but inasmuch as I currently
>>>seeing zero, any advance would be great.
>>>
>>>Again .. thanks in advance for all the time and effort!
>>>
>>>- Jan Allbright
>>>
>>>On 10/18/2016 07:36, Andrey Fedorov wrote:
>>>> Jan,
>>>>
>>>> As a general comment, CT is not the optimal modality for visualizing
>>>> brain soft tissue. If you have an MR scan, it would be more suitable
>>>> for this task.
>>>>
>>>> Were you looking to just segment the cortical surface, or something
>>>>else?
>>>>
>>>> Let us know about your experience learning from the tutorial.
>>>>
>>>> AF
>>>>
>>>> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole
>>>><[hidden email]> wrote:
>>>>> Hello Jan,
>>>>>
>>>>> There¹s a video tutorial available that should be helpful:
>>>>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>>>>
>>>>> Nicole
>>>>>
>>>>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I am a Vietnam veteran with a TBI.
>>>>>> I recently got a CT scan of the head and received a copy of the
>>>>>>images,
>>>>>> which I have successfully viewed via "Reviewer".
>>>>>> I got the idea of using Slicer to generate a mesh that I could feed
>>>>>>to a
>>>>>> 3D printer so that I could have a model of my damaged brain, but
>>>>>>Slicer
>>>>>> is not co-operating.
>>>>>> I load up the coronal view (DICOM), and it shows up in the three
>>>>>>views,
>>>>>> but the 3d rendering does not appear to function and since I don't
>>>>>>see
>>>>>> any error messages I am at a loss as to how to proceed.
>>>>>>
>>>>>> Any help from anyone would be greatly appreciated.
>>>>>>
>>>>>> - Jan Allbright
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>
>>_______________________________________________
>>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
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Re: Need help with application

Csaba Pinter-2

See STL export instructions in HowTo section of page

https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations

 

csaba

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Fernando Pérez-García
Sent: Wednesday, October 19, 2016 10:54
To: Andrey Fedorov <[hidden email]>
Cc: SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Need help with application

 

​@Andrey: you can generate the surface with the Segmentations module after you've edited your segmentation using the Segment Editor module.

 

Fernando​

 

2016-10-19 16:47 GMT+02:00 Andrey Fedorov <[hidden email]>:

Jan,

to get back to your original issue, if I understand it correctly -
"using Slicer to generate a mesh that I could feed to a 3D printer".

I recorded a quick screencast showing how to get 3d view of the kind
you want to see (if I understand it correctly):

http://www.screencast.com/t/I0TQS5Qcm (this is for MR, since I don't
have a sample head CT handy).

There are two parts - volume rendering, that can help you explore the
data, and surface extraction, which generates a triangulation that you
can save and potentially use for 3d printing.

As I was going over the demo, I realized that using Segment Editor
does not generate a surface that could be saved, so that is a caveat,
but hopefully this will help you a little bit to get going with your
data.

AF


On Wed, Oct 19, 2016 at 10:06 AM, Aucoin, Nicole <[hidden email]> wrote:
>
> Also: try out different Presets in the Display panel, there are some
> transfer functions that are better for various CT scans.
>
> Nicole
>
> On 10/19/16, 10:02 AM, "Aucoin, Nicole" <[hidden email]> wrote:
>
>>Hi Jan,
>>
>>It sounds like an issue with your video card combined with the 3D volume
>>rendering method. If you click on the red X at the bottom right, it should
>>bring up an error log that might give you more information. You can also
>>go into the Volume Rendering Module, the Rendering drop down menu in the
>>Display section has a few options (assumign that the eye icon next to the
>>Volume selector showing MRHead is open). Try the different rendering modes
>>and see if that helps.
>>Also, which version of Slicer are you using? (Slicer->About)
>>
>>Nicole
>>
>>On 10/19/16, 9:14 AM, "Jan Allbright" <[hidden email]> wrote:
>>
>>>I have followed the steps laid out in many "how-to" pages and also
>>>followed the video.
>>>At 10 minutes the demonstrator invokes the Volume Render and the head
>>>appears in the 3D window.
>>>In my case nothing happens .. no spinner, no error message, nothing.
>>>The other three windows function as advertised including brightness and
>>>contrast functions.
>>>ITK-SNAP pretty much responds the same way.
>>>I am thinking there must be something wrong with my data-set, but my
>>>understanding of DICOM data is very superficial.
>>>Is it possible that the data can be such that the standard views are OK
>>>but are somehow corrupted as to prevent the 3D rendering?
>>>This is from a Veterans Administration data-set. Could there be
>>>something missing?
>>>
>>>As to the choice of CT vs MRI, I have residual metallic fragments in my
>>>scalp that prohibit the MRI.
>>>
>>>Bone and Cortical imaging would be ideal but inasmuch as I currently
>>>seeing zero, any advance would be great.
>>>
>>>Again .. thanks in advance for all the time and effort!
>>>
>>>- Jan Allbright
>>>
>>>On 10/18/2016 07:36, Andrey Fedorov wrote:
>>>> Jan,
>>>>
>>>> As a general comment, CT is not the optimal modality for visualizing
>>>> brain soft tissue. If you have an MR scan, it would be more suitable
>>>> for this task.
>>>>
>>>> Were you looking to just segment the cortical surface, or something
>>>>else?
>>>>
>>>> Let us know about your experience learning from the tutorial.
>>>>
>>>> AF
>>>>
>>>> On Tue, Oct 18, 2016 at 10:04 AM, Aucoin, Nicole
>>>><[hidden email]> wrote:
>>>>> Hello Jan,
>>>>>
>>>>> There¹s a video tutorial available that should be helpful:
>>>>> https://www.youtube.com/watch?v=MKLWzD0PiIc
>>>>>
>>>>> Nicole
>>>>>
>>>>> On 10/18/16, 9:41 AM, "Jan Allbright" <[hidden email]> wrote:
>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I am a Vietnam veteran with a TBI.
>>>>>> I recently got a CT scan of the head and received a copy of the
>>>>>>images,
>>>>>> which I have successfully viewed via "Reviewer".
>>>>>> I got the idea of using Slicer to generate a mesh that I could feed
>>>>>>to a
>>>>>> 3D printer so that I could have a model of my damaged brain, but
>>>>>>Slicer
>>>>>> is not co-operating.
>>>>>> I load up the coronal view (DICOM), and it shows up in the three
>>>>>>views,
>>>>>> but the 3d rendering does not appear to function and since I don't
>>>>>>see
>>>>>> any error messages I am at a loss as to how to proceed.
>>>>>>
>>>>>> Any help from anyone would be greatly appreciated.
>>>>>>
>>>>>> - Jan Allbright
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>
>>_______________________________________________
>>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
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Re: Need help with application - Solved

Jan Allbright
In reply to this post by Jan Allbright
While none of the offered advice actually worked, this post came pretty
darn close and gave me the hint on how to actually get the task done ...

See the attached image.

- Jan Allbright

On 10/19/2016 06:37, Ramon F Herrera wrote:

> Jan:
>
>   Try the steps in the attached image.
>
> -RFH
>
> On Wed, Oct 19, 2016 at 01:14:41PM +0000, Jan Allbright wrote:
>> I have followed the steps laid out in many "how-to" pages and also
>> followed the video.
>> At 10 minutes the demonstrator invokes the Volume Render and the head
>> appears in the 3D window.
>> In my case nothing happens .. no spinner, no error message, nothing.
>> The other three windows function as advertised including brightness and
>> contrast functions.
>> ITK-SNAP pretty much responds the same way.
>> I am thinking there must be something wrong with my data-set, but my
>> understanding of DICOM data is very superficial.
>> Is it possible that the data can be such that the standard views are OK
>> but are somehow corrupted as to prevent the 3D rendering?
>> This is from a Veterans Administration data-set. Could there be
>> something missing?
>>
>> As to the choice of CT vs MRI, I have residual metallic fragments in my
>> scalp that prohibit the MRI.
>>
>> Bone and Cortical imaging would be ideal but inasmuch as I currently
>> seeing zero, any advance would be great.
>>
>> Again .. thanks in advance for all the time and effort!
>>
>> - Jan Allbright
>>

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