Create Colorful Dicom Series

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Create Colorful Dicom Series

Nicos Markides
Hello,

 I don't know if it's a stupid question but i got stuck ! My issue is when I'm creating the dicom series for the label map i got
from the segmentation using the EM Segmenter Module. The dicom series are all stored in
a grayscale format. Is there any other way of saving the label map in slices but the coloring information
to be retained ? And if not, do you know any efficient way to convert the grayscale image to RGB, because i need the colors
of the label map to be shown when i'm importing them to Matlab.

Thank u, Nikos

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Re: Create Colorful Dicom Series

Steve Pieper
Hi Nikos -

The color mapping slicer uses is described here:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Colors

You'll need to find a way to import these definitions into matlab and apply them to the dicom data after loading.

HTH,
Steve

On Fri, Jul 27, 2012 at 12:12 PM, Nicos Markides <[hidden email]> wrote:
Hello,

 I don't know if it's a stupid question but i got stuck ! My issue is when I'm creating the dicom series for the label map i got
from the segmentation using the EM Segmenter Module. The dicom series are all stored in
a grayscale format. Is there any other way of saving the label map in slices but the coloring information
to be retained ? And if not, do you know any efficient way to convert the grayscale image to RGB, because i need the colors
of the label map to be shown when i'm importing them to Matlab.

Thank u, Nikos

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resample scalar/vector/DWI transformation problem

Murat Maga

Hi All

 

I have volumes that I rotated using the manual transform tool. Now I want to save the reoriented dataset as a new volume. I use the resample scalar/vector/DWI module to do that. I specify the original as the input, create a new volume and then specify the transform node as the manual one I created. I leave everything else as it is.

 

When I execute the module I encounter either an empty volume, or a truncated one.  Below is an example of (top: original rotated, bottom: output from the module).

 

I use windows 7 64 bit nightly build from 7.25

 

Any suggestions highly appreciated.

 

Thanks,

M

 

 

 


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Re: resample scalar/vector/DWI transformation problem

Dominik Meier
Hi Murat

I recommend setting a reference volume to resample (one of the input options), ideally the image to which this one was registered. Choosing a reference will copy resolution and spatial orientation and thus ensure your FOV does not get clipped. If resolution of the reference is not to your liking, then first make a new copy by resampling the reference in place to a higher resolution and then feed that as the reference input when resampling your moving image.

alternatively you can set the FOV and resolution manually,but that tends to include a bit more trial and error than the above.

Best,
Dominik



On 27.07.12 20:05, Murat Maga wrote:

Hi All

 

I have volumes that I rotated using the manual transform tool. Now I want to save the reoriented dataset as a new volume. I use the resample scalar/vector/DWI module to do that. I specify the original as the input, create a new volume and then specify the transform node as the manual one I created. I leave everything else as it is.

 

When I execute the module I encounter either an empty volume, or a truncated one.  Below is an example of (top: original rotated, bottom: output from the module).

 

I use windows 7 64 bit nightly build from 7.25

 

Any suggestions highly appreciated.

 

Thanks,

M

 

 

 





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Nightly builds of Slicer

Murat Maga

Hi,

 

How do I download to a specific nightly build of Slicer. I need the Windows 64 bit binary from 7.25.

 

Thanks,

M

 


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Re: Nightly builds of Slicer

Steve Pieper
Hi Murat -

In general we don't keep all the nighties, but you might be able to
find what you are looking for here:

http://slicer.kitware.com/midas3/slicerpackages/view/advanced

it's linked off the midas page http://slicer.kitware.com which is the
back end for the slicer download page.

-Steve


On Sat, Jul 28, 2012 at 11:35 AM, Murat Maga <[hidden email]> wrote:

> Hi,
>
>
>
> How do I download to a specific nightly build of Slicer. I need the Windows
> 64 bit binary from 7.25.
>
>
>
> Thanks,
>
> M
>
>
>
>
> _______________________________________________
> 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: Nightly builds of Slicer

Andrey Fedorov
You could also look at CDash for Jul 25

http://slicer.cdash.org/index.php?project=Slicer4&date=2012-07-25

On Sat, Jul 28, 2012 at 12:45 PM, Steve Pieper <[hidden email]> wrote:

> Hi Murat -
>
> In general we don't keep all the nighties, but you might be able to
> find what you are looking for here:
>
> http://slicer.kitware.com/midas3/slicerpackages/view/advanced
>
> it's linked off the midas page http://slicer.kitware.com which is the
> back end for the slicer download page.
>
> -Steve
>
>
> On Sat, Jul 28, 2012 at 11:35 AM, Murat Maga <[hidden email]> wrote:
>> Hi,
>>
>>
>>
>> How do I download to a specific nightly build of Slicer. I need the Windows
>> 64 bit binary from 7.25.
>>
>>
>>
>> Thanks,
>>
>> M
>>
>>
>>
>>
>> _______________________________________________
>> 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
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