Lb invalid tag

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Lb invalid tag

Panagiotis Foteinos
Hello all.

I open a multi-labeled mha brain image and I see something I do not understand.

When I drag the mouse on a brain slice, the lower left corner of Slicer reads "Lb: 608 invalid" or generaly "Lb: <a positive number> invalid". What does "invalid" mean? Why are there two components for the attribute "Lb" (i.e., one that states the label number and one that states "invalid")? How should I interpret it?

I also observed that when I drag the mouse on the surface of a brain slice, I do not have any problem: Slicer reads "Lb: <a positive number>" without any "invalid" component.

Does someone have an idea?


Best Regards,
Panagiotis Foteinos




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Re: Lb invalid tag

Andrey Fedorov
I think this may be because the colormap assigned to our label volume
does not have a color for that particular label value.

On Fri, Dec 17, 2010 at 19:18, Panagiotis Foteinos <[hidden email]> wrote:

> Hello all.
>
> I open a multi-labeled mha brain image and I see something I do not
> understand.
>
> When I drag the mouse on a brain slice, the lower left corner of Slicer
> reads "Lb: 608 invalid" or generaly "Lb: <a positive number> invalid". What
> does "invalid" mean? Why are there two components for the attribute "Lb"
> (i.e., one that states the label number and one that states "invalid")? How
> should I interpret it?
>
> I also observed that when I drag the mouse on the surface of a brain slice,
> I do not have any problem: Slicer reads "Lb: <a positive number>" without
> any "invalid" component.
>
> Does someone have an idea?
>
>
> Best Regards,
> Panagiotis Foteinos
>
>
>
>
> _______________________________________________
> 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: Lb invalid tag

pieper
Administrator
yes, as Andrey points out, the selected colormap doesn't have anything
defined for those numerical values.  You probably want to go into the
Volumes module, select the label map, and pick the FreeSurfer Labels
color table to get the mapping from numbers to the standard freesurfer
names and colors.

Best,
Steve

On 12/17/2010 07:36 PM, Andriy Fedorov wrote:

> I think this may be because the colormap assigned to our label volume
> does not have a color for that particular label value.
>
> On Fri, Dec 17, 2010 at 19:18, Panagiotis Foteinos<[hidden email]>  wrote:
>> Hello all.
>>
>> I open a multi-labeled mha brain image and I see something I do not
>> understand.
>>
>> When I drag the mouse on a brain slice, the lower left corner of Slicer
>> reads "Lb: 608 invalid" or generaly "Lb:<a positive number>  invalid". What
>> does "invalid" mean? Why are there two components for the attribute "Lb"
>> (i.e., one that states the label number and one that states "invalid")? How
>> should I interpret it?
>>
>> I also observed that when I drag the mouse on the surface of a brain slice,
>> I do not have any problem: Slicer reads "Lb:<a positive number>" without
>> any "invalid" component.
>>
>> Does someone have an idea?
>>
>>
>> Best Regards,
>> Panagiotis Foteinos
>>
>>
>>
>>
>> _______________________________________________
>> 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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Re: Lb invalid tag

Panagiotis Foteinos
Thanks for the replies.

Would it hurt, if I completely ignored these "invalid" statements? The value of the pixels (i.e., the GetPixel() result) will correctly correspond to the label, right? I would just not be able to see "different" colors in Slicer for "invalid" labels, correct? I am just making sure.

Thank you,
Panagiotis Foteinos

On Fri, Dec 17, 2010 at 8:31 PM, Steve Pieper <[hidden email]> wrote:
yes, as Andrey points out, the selected colormap doesn't have anything defined for those numerical values.  You probably want to go into the Volumes module, select the label map, and pick the FreeSurfer Labels color table to get the mapping from numbers to the standard freesurfer names and colors.

Best,
Steve


On 12/17/2010 07:36 PM, Andriy Fedorov wrote:
I think this may be because the colormap assigned to our label volume
does not have a color for that particular label value.

On Fri, Dec 17, 2010 at 19:18, Panagiotis Foteinos<[hidden email]>  wrote:
Hello all.

I open a multi-labeled mha brain image and I see something I do not
understand.

When I drag the mouse on a brain slice, the lower left corner of Slicer
reads "Lb: 608 invalid" or generaly "Lb:<a positive number>  invalid". What
does "invalid" mean? Why are there two components for the attribute "Lb"
(i.e., one that states the label number and one that states "invalid")? How
should I interpret it?

I also observed that when I drag the mouse on the surface of a brain slice,
I do not have any problem: Slicer reads "Lb:<a positive number>" without
any "invalid" component.

Does someone have an idea?


Best Regards,
Panagiotis Foteinos




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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: Lb invalid tag

pieper
Administrator
No, in most cases it shouldn't hurt if the labels have invalid names as
long as the numbers are correct.  Most modules will ignore the names but
some, like Model Maker, use the names and colors to set defaults for any
structures you create.

-Steve

On 12/18/2010 03:36 PM, Panagiotis Foteinos wrote:

> Thanks for the replies.
>
> Would it hurt, if I completely ignored these "invalid" statements? The
> value of the pixels (i.e., the GetPixel() result) will correctly
> correspond to the label, right? I would just not be able to see
> "different" colors in Slicer for "invalid" labels, correct? I am just
> making sure.
>
> Thank you,
> Panagiotis Foteinos
>
> On Fri, Dec 17, 2010 at 8:31 PM, Steve Pieper <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     yes, as Andrey points out, the selected colormap doesn't have
>     anything defined for those numerical values.  You probably want to
>     go into the Volumes module, select the label map, and pick the
>     FreeSurfer Labels color table to get the mapping from numbers to the
>     standard freesurfer names and colors.
>
>     Best,
>     Steve
>
>
>     On 12/17/2010 07:36 PM, Andriy Fedorov wrote:
>
>         I think this may be because the colormap assigned to our label
>         volume
>         does not have a color for that particular label value.
>
>         On Fri, Dec 17, 2010 at 19:18, Panagiotis
>         Foteinos<[hidden email] <mailto:[hidden email]>>  wrote:
>
>             Hello all.
>
>             I open a multi-labeled mha brain image and I see something I
>             do not
>             understand.
>
>             When I drag the mouse on a brain slice, the lower left
>             corner of Slicer
>             reads "Lb: 608 invalid" or generaly "Lb:<a positive number>
>               invalid". What
>             does "invalid" mean? Why are there two components for the
>             attribute "Lb"
>             (i.e., one that states the label number and one that states
>             "invalid")? How
>             should I interpret it?
>
>             I also observed that when I drag the mouse on the surface of
>             a brain slice,
>             I do not have any problem: Slicer reads "Lb:<a positive
>             number>" without
>             any "invalid" component.
>
>             Does someone have an idea?
>
>
>             Best Regards,
>             Panagiotis Foteinos
>
>
>
>
>             _______________________________________________
>             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] <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
>
>
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