Cross-section image quality

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Cross-section image quality

Kannan U V
Hi,
I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
the trouble figuring out the following.

1) The image quality of the cross section rendered is very coarse
compared to the original image. How do I get the full resolution
rendered. There is an Slicer2 tcl script that is not compatible any
longer.
2) The cross section image rendered is looks different (histogram). I
am using grey lookup table. Is there any quantitative way to set the
grey level apart form window/level?

Thanks,
Kannan
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Re: Cross-section image quality

pieper
Administrator
Hi Kannan -

The image is resampled to the size of the slice view - so if you are
looking at the textured 3D plane it will only have the amount of
information corresponding to the size of the slice view.  If you are
trying to see the 3D view at high resolution, one trick you can try is
to switch to Red Slice Only layout to make the slice big.  Then switch
to 3D only view and it will use the old window size for the texture.

Window/level should allow you to get the exact grayscale display for the
8 bit dataset.

-Steve

On 01/06/2011 02:10 PM, Kannan U V wrote:

> Hi,
> I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
> the trouble figuring out the following.
>
> 1) The image quality of the cross section rendered is very coarse
> compared to the original image. How do I get the full resolution
> rendered. There is an Slicer2 tcl script that is not compatible any
> longer.
> 2) The cross section image rendered is looks different (histogram). I
> am using grey lookup table. Is there any quantitative way to set the
> grey level apart form window/level?
>
> Thanks,
> Kannan
> _______________________________________________
> 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: Cross-section image quality

Kannan U V
Hi Steve,
It works great, but would it be possible to render the 2D slice with
an even finer resolution. Is it possible to set the plane to render
from a higher resolution mip-map rather using the one currently in
view in the red box?

Thanks,
Kannan

On Thu, Jan 6, 2011 at 4:59 PM, Steve Pieper <[hidden email]> wrote:

> Hmm.. if you go to a compare view layout and collapse the bottom frame and
> side panel (little triangles) you can get the attached....
>
> HTH,
> Steve
>
> On 01/06/2011 04:43 PM, Kannan U V wrote:
>>
>> Hi Steve,
>> Thanks for your quick reply. I have a volume rendering alongside the
>> cross section view. Is there a way to have just Red Slice and close
>> the green and yellow slices? Or a python/TCL way? The visualization
>> need not even be very interactive.
>>
>> Thanks,
>> Kannan
>>
>>
>> On Thu, Jan 6, 2011 at 2:58 PM, Steve Pieper<[hidden email]>
>>  wrote:
>>>
>>> Hi Kannan -
>>>
>>> The image is resampled to the size of the slice view - so if you are
>>> looking
>>> at the textured 3D plane it will only have the amount of information
>>> corresponding to the size of the slice view.  If you are trying to see
>>> the
>>> 3D view at high resolution, one trick you can try is to switch to Red
>>> Slice
>>> Only layout to make the slice big.  Then switch to 3D only view and it
>>> will
>>> use the old window size for the texture.
>>>
>>> Window/level should allow you to get the exact grayscale display for the
>>> 8
>>> bit dataset.
>>>
>>> -Steve
>>>
>>> On 01/06/2011 02:10 PM, Kannan U V wrote:
>>>>
>>>> Hi,
>>>> I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
>>>> the trouble figuring out the following.
>>>>
>>>> 1) The image quality of the cross section rendered is very coarse
>>>> compared to the original image. How do I get the full resolution
>>>> rendered. There is an Slicer2 tcl script that is not compatible any
>>>> longer.
>>>> 2) The cross section image rendered is looks different (histogram). I
>>>> am using grey lookup table. Is there any quantitative way to set the
>>>> grey level apart form window/level?
>>>>
>>>> Thanks,
>>>> Kannan
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>



--
Thanks,
Kannan
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Re: Cross-section image quality

Kannan U V
Btw. this is the figure I am trying to render with the coronal section
at a higher resolution.

Thanks,
Kannan

On Thu, Jan 6, 2011 at 5:35 PM, Kannan U V <[hidden email]> wrote:

> Hi Steve,
> It works great, but would it be possible to render the 2D slice with
> an even finer resolution. Is it possible to set the plane to render
> from a higher resolution mip-map rather using the one currently in
> view in the red box?
>
> Thanks,
> Kannan
>
> On Thu, Jan 6, 2011 at 4:59 PM, Steve Pieper <[hidden email]> wrote:
>> Hmm.. if you go to a compare view layout and collapse the bottom frame and
>> side panel (little triangles) you can get the attached....
>>
>> HTH,
>> Steve
>>
>> On 01/06/2011 04:43 PM, Kannan U V wrote:
>>>
>>> Hi Steve,
>>> Thanks for your quick reply. I have a volume rendering alongside the
>>> cross section view. Is there a way to have just Red Slice and close
>>> the green and yellow slices? Or a python/TCL way? The visualization
>>> need not even be very interactive.
>>>
>>> Thanks,
>>> Kannan
>>>
>>>
>>> On Thu, Jan 6, 2011 at 2:58 PM, Steve Pieper<[hidden email]>
>>>  wrote:
>>>>
>>>> Hi Kannan -
>>>>
>>>> The image is resampled to the size of the slice view - so if you are
>>>> looking
>>>> at the textured 3D plane it will only have the amount of information
>>>> corresponding to the size of the slice view.  If you are trying to see
>>>> the
>>>> 3D view at high resolution, one trick you can try is to switch to Red
>>>> Slice
>>>> Only layout to make the slice big.  Then switch to 3D only view and it
>>>> will
>>>> use the old window size for the texture.
>>>>
>>>> Window/level should allow you to get the exact grayscale display for the
>>>> 8
>>>> bit dataset.
>>>>
>>>> -Steve
>>>>
>>>> On 01/06/2011 02:10 PM, Kannan U V wrote:
>>>>>
>>>>> Hi,
>>>>> I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
>>>>> the trouble figuring out the following.
>>>>>
>>>>> 1) The image quality of the cross section rendered is very coarse
>>>>> compared to the original image. How do I get the full resolution
>>>>> rendered. There is an Slicer2 tcl script that is not compatible any
>>>>> longer.
>>>>> 2) The cross section image rendered is looks different (histogram). I
>>>>> am using grey lookup table. Is there any quantitative way to set the
>>>>> grey level apart form window/level?
>>>>>
>>>>> Thanks,
>>>>> Kannan
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>
>>>
>>>
>>
>
>
>
> --
> Thanks,
> Kannan
>


--
Thanks,
Kannan

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Re: Cross-section image quality

Kannan U V
Hi Steve,
I tried switching from the red only view to 3D only view and I get an
image that looks like this. It is cropped and doesn't have the
resolution it has on the red only layout too.

Thanks,
Kannan

On Thu, Jan 6, 2011 at 5:37 PM, Kannan U V <[hidden email]> wrote:

> Btw. this is the figure I am trying to render with the coronal section
> at a higher resolution.
>
> Thanks,
> Kannan
>
> On Thu, Jan 6, 2011 at 5:35 PM, Kannan U V <[hidden email]> wrote:
>> Hi Steve,
>> It works great, but would it be possible to render the 2D slice with
>> an even finer resolution. Is it possible to set the plane to render
>> from a higher resolution mip-map rather using the one currently in
>> view in the red box?
>>
>> Thanks,
>> Kannan
>>
>> On Thu, Jan 6, 2011 at 4:59 PM, Steve Pieper <[hidden email]> wrote:
>>> Hmm.. if you go to a compare view layout and collapse the bottom frame and
>>> side panel (little triangles) you can get the attached....
>>>
>>> HTH,
>>> Steve
>>>
>>> On 01/06/2011 04:43 PM, Kannan U V wrote:
>>>>
>>>> Hi Steve,
>>>> Thanks for your quick reply. I have a volume rendering alongside the
>>>> cross section view. Is there a way to have just Red Slice and close
>>>> the green and yellow slices? Or a python/TCL way? The visualization
>>>> need not even be very interactive.
>>>>
>>>> Thanks,
>>>> Kannan
>>>>
>>>>
>>>> On Thu, Jan 6, 2011 at 2:58 PM, Steve Pieper<[hidden email]>
>>>>  wrote:
>>>>>
>>>>> Hi Kannan -
>>>>>
>>>>> The image is resampled to the size of the slice view - so if you are
>>>>> looking
>>>>> at the textured 3D plane it will only have the amount of information
>>>>> corresponding to the size of the slice view.  If you are trying to see
>>>>> the
>>>>> 3D view at high resolution, one trick you can try is to switch to Red
>>>>> Slice
>>>>> Only layout to make the slice big.  Then switch to 3D only view and it
>>>>> will
>>>>> use the old window size for the texture.
>>>>>
>>>>> Window/level should allow you to get the exact grayscale display for the
>>>>> 8
>>>>> bit dataset.
>>>>>
>>>>> -Steve
>>>>>
>>>>> On 01/06/2011 02:10 PM, Kannan U V wrote:
>>>>>>
>>>>>> Hi,
>>>>>> I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
>>>>>> the trouble figuring out the following.
>>>>>>
>>>>>> 1) The image quality of the cross section rendered is very coarse
>>>>>> compared to the original image. How do I get the full resolution
>>>>>> rendered. There is an Slicer2 tcl script that is not compatible any
>>>>>> longer.
>>>>>> 2) The cross section image rendered is looks different (histogram). I
>>>>>> am using grey lookup table. Is there any quantitative way to set the
>>>>>> grey level apart form window/level?
>>>>>>
>>>>>> Thanks,
>>>>>> Kannan
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>> --
>> Thanks,
>> Kannan
>>
>
>
>
> --
> Thanks,
> Kannan
>


--
Thanks,
Kannan

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Re: Cross-section image quality

pieper
Administrator
Well, it's certainly possible to make that happen, but you would need to
write a little script for it - it would need to disconnect the default
slice rendering pipeline and explicitly set the resolution you need.  If
you want to go that route I can send you some pointers...  It would mean
setting the Dimensions field of the SliceNode and making sure that it
doesn't get overridden again by GUI events.

Best,
Steve


On 01/06/2011 05:52 PM, Kannan U V wrote:

> Hi Steve,
> I tried switching from the red only view to 3D only view and I get an
> image that looks like this. It is cropped and doesn't have the
> resolution it has on the red only layout too.
>
> Thanks,
> Kannan
>
> On Thu, Jan 6, 2011 at 5:37 PM, Kannan U V<[hidden email]>  wrote:
>> Btw. this is the figure I am trying to render with the coronal section
>> at a higher resolution.
>>
>> Thanks,
>> Kannan
>>
>> On Thu, Jan 6, 2011 at 5:35 PM, Kannan U V<[hidden email]>  wrote:
>>> Hi Steve,
>>> It works great, but would it be possible to render the 2D slice with
>>> an even finer resolution. Is it possible to set the plane to render
>>> from a higher resolution mip-map rather using the one currently in
>>> view in the red box?
>>>
>>> Thanks,
>>> Kannan
>>>
>>> On Thu, Jan 6, 2011 at 4:59 PM, Steve Pieper<[hidden email]>  wrote:
>>>> Hmm.. if you go to a compare view layout and collapse the bottom frame and
>>>> side panel (little triangles) you can get the attached....
>>>>
>>>> HTH,
>>>> Steve
>>>>
>>>> On 01/06/2011 04:43 PM, Kannan U V wrote:
>>>>>
>>>>> Hi Steve,
>>>>> Thanks for your quick reply. I have a volume rendering alongside the
>>>>> cross section view. Is there a way to have just Red Slice and close
>>>>> the green and yellow slices? Or a python/TCL way? The visualization
>>>>> need not even be very interactive.
>>>>>
>>>>> Thanks,
>>>>> Kannan
>>>>>
>>>>>
>>>>> On Thu, Jan 6, 2011 at 2:58 PM, Steve Pieper<[hidden email]>
>>>>>   wrote:
>>>>>>
>>>>>> Hi Kannan -
>>>>>>
>>>>>> The image is resampled to the size of the slice view - so if you are
>>>>>> looking
>>>>>> at the textured 3D plane it will only have the amount of information
>>>>>> corresponding to the size of the slice view.  If you are trying to see
>>>>>> the
>>>>>> 3D view at high resolution, one trick you can try is to switch to Red
>>>>>> Slice
>>>>>> Only layout to make the slice big.  Then switch to 3D only view and it
>>>>>> will
>>>>>> use the old window size for the texture.
>>>>>>
>>>>>> Window/level should allow you to get the exact grayscale display for the
>>>>>> 8
>>>>>> bit dataset.
>>>>>>
>>>>>> -Steve
>>>>>>
>>>>>> On 01/06/2011 02:10 PM, Kannan U V wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>> I am trying to visualize a 2369x1667x210 sized 8-bit dataset. I have
>>>>>>> the trouble figuring out the following.
>>>>>>>
>>>>>>> 1) The image quality of the cross section rendered is very coarse
>>>>>>> compared to the original image. How do I get the full resolution
>>>>>>> rendered. There is an Slicer2 tcl script that is not compatible any
>>>>>>> longer.
>>>>>>> 2) The cross section image rendered is looks different (histogram). I
>>>>>>> am using grey lookup table. Is there any quantitative way to set the
>>>>>>> grey level apart form window/level?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Kannan
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Thanks,
>>> Kannan
>>>
>>
>>
>>
>> --
>> Thanks,
>> Kannan
>>
>
>
>
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Re: Cross-section image quality

Kannan U V

Hi steve,
That would be great. Give me some pointers how to do that, I will give it a try

Thanks,
Kannan

On Jan 6, 2011 7:36 PM, "Steve Pieper" <[hidden email]> wrote:

Well, it's certainly possible to make that happen, but you would need to write a little script for it - it would need to disconnect the default slice rendering pipeline and explicitly set the resolution you need.  If you want to go that route I can send you some pointers...  It would mean setting the Dimensions field of the SliceNode and making sure that it doesn't get overridden again by GUI events.

Best,
Steve




On 01/06/2011 05:52 PM, Kannan U V wrote:
>
> Hi Steve,
> I tried switching from the red only vie...


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Re: Cross-section image quality

pieper
Administrator
Hi Kannan -

Here's an easy hack that may do what you need.  Bring up the tcl console
and type in the following two commands:

  MRMLWatcher #auto
  $::MRML(Red) SetDimensions 2369 1667 1

You should see the Red viewer zoom to a corner and the 3D texture
quality improve.  If you move the mouse over the Red viewer the
dimensions will reset to the window size.

Best,
Steve

On 01/06/2011 07:46 PM, Kannan U V wrote:

> Hi steve,
> That would be great. Give me some pointers how to do that, I will give
> it a try
>
> Thanks,
> Kannan
>
>> On Jan 6, 2011 7:36 PM, "Steve Pieper" <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Well, it's certainly possible to make that happen, but you would need
>> to write a little script for it - it would need to disconnect the
>> default slice rendering pipeline and explicitly set the resolution you
>> need.  If you want to go that route I can send you some pointers...
>>  It would mean setting the Dimensions field of the SliceNode and
>> making sure that it doesn't get overridden again by GUI events.
>>
>> Best,
>> Steve
>>
>>
>>
>>
>> On 01/06/2011 05:52 PM, Kannan U V wrote:
>> >
>> > Hi Steve,
>> > I tried switching from the red only vie...
>>
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