Image resolution

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Image resolution

Samuele Zampini
Dear All,

I am trying to extract a certain area (I would like to reconstruct the nasal airways)
from a CT-scan.

The question is that, when I open it with 3D-Slicer it has a terrible resolution
(see the screenshot attached: it is in blue, but in grey it's the same!).

Could you guess why it is so low-resolution?

Also, another question: Im a very beginner. Where can I find a good tutorial to
begin with 3D-Slicer?

Thanks a lot,

--
                                                                                                      Samuele Z 

____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


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Re: Image resolution

Kikinis, Ron,M.D.
Hi,

The 3d viewer displays at the resolution of the display in the slice
viewers. In your screen snapshot you have the 2d slice viewers collapsed.
Please try the following: Go to the "red slice only" layout and use the
fit to window function in the slice viewer? Then switch to "3D only"
layout.

Please let me know if that works.

Ron

On 9/30/10 4:19 AM, Samuele Zampini wrote:

> Dear All,
>
> I am trying to extract a certain area (I would like to reconstruct the
> nasal airways)
> from a CT-scan.
>
> The question is that, when I open it with 3D-Slicer it has a terrible
> resolution
> (see the screenshot attached: it is in blue, but in grey it's the same!).
>
> Could you guess why it is so low-resolution?
>
> Also, another question: Im a very beginner. Where can I find a good
> tutorial to
> begin with 3D-Slicer?
>
> Thanks a lot,
>
> --
>
>                                Samuele Z
>
> ____________________________________________________________________
>
>    .~.
>    /V\       L   I   N   U   X
>   // \\          I S    T H E
>   /(   )\           W A Y
>   ^^-^^
>   cell phone :  +393473426510       e.mail: [hidden email]
> <mailto:[hidden email]>
>   home        :   +390331823927       www: samiam1000.spaces.live.com
> <http://samiam1000.spaces.live.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
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Re: Image resolution

swallace
In reply to this post by Samuele Zampini
You can see what parameters you are working with by checking out the
Volumes module, under Info.

Changing windowing parameters can also help improve visualization- again
these are under the Volumes module, under Display. There CT specific
presets that might help clean things up.

Please also find Slicer tutorials here:

http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials

If you're just beginning, the 3Minute, Visualization and Interactive
Editor tutorials will be a nice start.


On Thu, September 30, 2010 4:19 am, Samuele Zampini wrote:

> Dear All,
>
> I am trying to extract a certain area (I would like to reconstruct the
> nasal
> airways)
> from a CT-scan.
>
> The question is that, when I open it with 3D-Slicer it has a terrible
> resolution
> (see the screenshot attached: it is in blue, but in grey it's the same!).
>
> Could you guess why it is so low-resolution?
>
> Also, another question: Im a very beginner. Where can I find a good
> tutorial
> to
> begin with 3D-Slicer?
>
> Thanks a lot,
>
> --
>
>                           Samuele Z
>
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.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: Image resolution

Samuele Zampini
Hi All,

I think that Ron gave me the right solution. The question is that Im not very familiar 
with Slicer and I am finding it difficult to follow his advice.

I mean: I have a folder with all the DICOM image in it. Then I select "Add volume"
from the File menu and I get what you can see in the picture I attached in my 1st
email.
I do as Ron suggested, but I get nothing but a bigger image (see attachments),
without any 3D reconstruction. How can I get it??

Furthermore, another point: I carefully read the 1st tutorial at this address
but in the file that I download there is a "volume file" that I do not have starting
from my DICOM series.
What should I do?

Thanks,

Samuele



On Thu, Sep 30, 2010 at 1:14 PM, <[hidden email]> wrote:
You can see what parameters you are working with by checking out the
Volumes module, under Info.

Changing windowing parameters can also help improve visualization- again
these are under the Volumes module, under Display. There CT specific
presets that might help clean things up.

Please also find Slicer tutorials here:

http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials

If you're just beginning, the 3Minute, Visualization and Interactive
Editor tutorials will be a nice start.


On Thu, September 30, 2010 4:19 am, Samuele Zampini wrote:
> Dear All,
>
> I am trying to extract a certain area (I would like to reconstruct the
> nasal
> airways)
> from a CT-scan.
>
> The question is that, when I open it with 3D-Slicer it has a terrible
> resolution
> (see the screenshot attached: it is in blue, but in grey it's the same!).
>
> Could you guess why it is so low-resolution?
>
> Also, another question: Im a very beginner. Where can I find a good
> tutorial
> to
> begin with 3D-Slicer?
>
> Thanks a lot,
>
> --
>
>                           Samuele Z
>
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.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



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.




--
                                                                                         Samuele Zampini
____________________________________________________________________

  .~.                               
  /V\       L   I   N   U   X    
 // \\          I S    T H E
 /(   )\           W A Y
 ^^-^^
 cell phone :  +393473426510       e.mail:  [hidden email]
 home        :   +390331823927       www:   samiam1000.spaces.live.com


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Image resolution

swallace
In reply to this post by Samuele Zampini
You can adjust the windowing of the CT image once you have loaded the
dicom in order to better visualize the data; it looks like you are in
CT-bone windowing, but you can use CT-brain windowing to better visualize
cortical structures.

The 3D viewer allows you to visualize the loaded data in all 3 planes at
once. You must use the pertinent modules to create a 3D model of your
structure of interest. Using the Interactive Editor and Model Maker module
is one way to do this, but other options also available.

As far as the tutorials, the example datasets provided are simply for
training.

I hope this helps in answering your questions, and please see our
documentation wiki for more information:

http://www.slicer.org/slicerWiki/index.php/Documentation-3.6

...and don't hesitate to consult the user list as well.

Stuart



On Thu, September 30, 2010 1:18 pm, Samuele Zampini wrote:

> Hi All,
>
> I think that Ron gave me the right solution. The question is that Im not
> very familiar
> with Slicer and I am finding it difficult to follow his advice.
>
> I mean: I have a folder with all the DICOM image in it. Then I select "Add
> volume"
> from the File menu and I get what you can see in the picture I attached in
> my 1st
> email.
> I do as Ron suggested, but I get nothing but a bigger image (see
> attachments),
> without any 3D reconstruction. How can I get it??
>
> Furthermore, another point: I carefully read the 1st tutorial at this
> address
> http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials
> ,
> but in the file that I download there is a "volume file" that I do not
> have
> starting
> from my DICOM series.
> What should I do?
>
> Thanks,
>
> Samuele
>
>
>
> On Thu, Sep 30, 2010 at 1:14 PM, <[hidden email]> wrote:
>
>> You can see what parameters you are working with by checking out the
>> Volumes module, under Info.
>>
>> Changing windowing parameters can also help improve visualization- again
>> these are under the Volumes module, under Display. There CT specific
>> presets that might help clean things up.
>>
>> Please also find Slicer tutorials here:
>>
>>
>> http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials
>>
>> If you're just beginning, the 3Minute, Visualization and Interactive
>> Editor tutorials will be a nice start.
>>
>>
>> On Thu, September 30, 2010 4:19 am, Samuele Zampini wrote:
>> > Dear All,
>> >
>> > I am trying to extract a certain area (I would like to reconstruct the
>> > nasal
>> > airways)
>> > from a CT-scan.
>> >
>> > The question is that, when I open it with 3D-Slicer it has a terrible
>> > resolution
>> > (see the screenshot attached: it is in blue, but in grey it's the
>> same!).
>> >
>> > Could you guess why it is so low-resolution?
>> >
>> > Also, another question: Im a very beginner. Where can I find a good
>> > tutorial
>> > to
>> > begin with 3D-Slicer?
>> >
>> > Thanks a lot,
>> >
>> > --
>> >
>> >                           Samuele Z
>> >
>> > ____________________________________________________________________
>> >
>> >   .~.
>> >   /V\       L   I   N   U   X
>> >  // \\          I S    T H E
>> >  /(   )\           W A Y
>> >  ^^-^^
>> >  cell phone :  +393473426510       e.mail:  [hidden email]
>> >  home        :   +390331823927       www:   samiam1000.spaces.live.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
>>
>>
>>
>> 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.
>>
>>
>
>
> --
>
>              Samuele Zampini
> ____________________________________________________________________
>
>   .~.
>   /V\       L   I   N   U   X
>  // \\          I S    T H E
>  /(   )\           W A Y
>  ^^-^^
>  cell phone :  +393473426510       e.mail:  [hidden email]
>  home        :   +390331823927       www:   samiam1000.spaces.live.com
>

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Re: Image resolution

Dr. András Jakab
In reply to this post by Kikinis, Ron,M.D.
Hi

I always wondered what was behind this phenomenon - is there a specific reason for this? I mean, in many cases, it does not seem advantageous that the 2d slice
views have to be enlarged to get proper resolution for the 3d view, e.g., when tiny lesions have to be visualized on brain MRI. Is there a way to override this (without switching to the 3d only view)?

Thank you
András


On Thu, Sep 30, 2010 at 1:10 PM, Ron Kikinis <[hidden email]> wrote:
Hi,

The 3d viewer displays at the resolution of the display in the slice
viewers. In your screen snapshot you have the 2d slice viewers collapsed.
Please try the following: Go to the "red slice only" layout and use the
fit to window function in the slice viewer? Then switch to "3D only"
layout.

Please let me know if that works.

Ron

On 9/30/10 4:19 AM, Samuele Zampini wrote:
> Dear All,
>
> I am trying to extract a certain area (I would like to reconstruct the
> nasal airways)
> from a CT-scan.
>
> The question is that, when I open it with 3D-Slicer it has a terrible
> resolution
> (see the screenshot attached: it is in blue, but in grey it's the same!).
>
> Could you guess why it is so low-resolution?
>
> Also, another question: Im a very beginner. Where can I find a good
> tutorial to
> begin with 3D-Slicer?
>
> Thanks a lot,
>
> --
>
>                                Samuele Z
>
> ____________________________________________________________________
>
>    .~.
>    /V\       L   I   N   U   X
>   // \\          I S    T H E
>   /(   )\           W A Y
>   ^^-^^
>   cell phone :  +393473426510       e.mail: [hidden email]
> <mailto:[hidden email]>
>   home        :   +390331823927       www: samiam1000.spaces.live.com
> <http://samiam1000.spaces.live.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
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Re: Image resolution

pieper
Administrator
In slicer3 the exact image that is formated for the slice view is used
for the texture (that is why the texture resolution is low when the
slice viewer is small).  It would be a nice feature decouple those two
-- perhaps for slicer4...

-Steve

On 09/30/2010 03:47 PM, András Jakab MD wrote:

> Hi
>
> I always wondered what was behind this phenomenon - is there a specific
> reason for this? I mean, in many cases, it does not seem advantageous
> that the 2d slice
> views have to be enlarged to get proper resolution for the 3d view,
> e.g., when tiny lesions have to be visualized on brain MRI. Is there a
> way to override this (without switching to the 3d only view)?
>
> Thank you
> András
>
>
> On Thu, Sep 30, 2010 at 1:10 PM, Ron Kikinis <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi,
>
>     The 3d viewer displays at the resolution of the display in the slice
>     viewers. In your screen snapshot you have the 2d slice viewers
>     collapsed.
>     Please try the following: Go to the "red slice only" layout and use the
>     fit to window function in the slice viewer? Then switch to "3D only"
>     layout.
>
>     Please let me know if that works.
>
>     Ron
>
>     On 9/30/10 4:19 AM, Samuele Zampini wrote:
>      > Dear All,
>      >
>      > I am trying to extract a certain area (I would like to
>     reconstruct the
>      > nasal airways)
>      > from a CT-scan.
>      >
>      > The question is that, when I open it with 3D-Slicer it has a terrible
>      > resolution
>      > (see the screenshot attached: it is in blue, but in grey it's the
>     same!).
>      >
>      > Could you guess why it is so low-resolution?
>      >
>      > Also, another question: Im a very beginner. Where can I find a good
>      > tutorial to
>      > begin with 3D-Slicer?
>      >
>      > Thanks a lot,
>      >
>      > --
>      >
>      >                                Samuele Z
>      >
>      > ____________________________________________________________________
>      >
>      >    .~.
>      >    /V\       L   I   N   U   X
>      >   // \\          I S    T H E
>      >   /(   )\           W A Y
>      >   ^^-^^
>      >   cell phone :  +393473426510       e.mail:
>     [hidden email] <mailto:[hidden email]>
>      > <mailto:[hidden email] <mailto:[hidden email]>>
>      >   home        :   +390331823927       www:
>     samiam1000.spaces.live.com <http://samiam1000.spaces.live.com>
>      > <http://samiam1000.spaces.live.com>
>      >
>      >
>      >
>      > _______________________________________________
>      > slicer-users mailing list
>      > [hidden email] <mailto:[hidden email]>
>      > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>      > To unsubscribe: send email to
>     [hidden email]
>     <mailto:[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
>     <http://www.spl.harvard.edu/%7Ekikinis>
>     _______________________________________________
>     slicer-users mailing list
>     [hidden email] <mailto:[hidden email]>
>     http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>     To unsubscribe: send email to
>     [hidden email]
>     <mailto:[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
_______________________________________________
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