Saving Volumes

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Saving Volumes

Kyzyl Herzog
Hello everyone,

I'm experiencing some behavior in Slicer that has me somewhat confused. If I perform the following workflow:

1. Open slicer
2. Add two volumes (for now just one image each, 12 slices.)
3. Perform a B-Spline registration, registering the DTI image to the DCE image, creating a new volume for the output.
NB: At this point I am able to fade between the registered DTI image and the original DTI image, noting that an obvious transformation has occurred.

4. Save the scene, as well as the output volume (as nrrd).
5. Close slicer and re-open the scene file.

Then when I go back and compare the transformed image to the original, there is no difference. From here, if I re-calculate/re-apply the transformation, no change occurs in the image.

Also, once this condition occurs, nothing short of completely closing slicer will allow me to register and view the changes.

Is this known/intended behavior in Slicer? If so is there a way I can get around it? All I want to do is set up a scene with several sets of DTI/DCE images and their registered volumes, without having to re-calculate/re-sample them when  open it up again.

I'm using Slicer 3.4.1.0, WinXP SP3.


Thanks,

Kyzyl

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Re: Saving Volumes

Kyzyl Herzog
Anybody?

On Thu, Feb 11, 2010 at 2:49 PM, Kyzyl Herzog <[hidden email]> wrote:
Hello everyone,

I'm experiencing some behavior in Slicer that has me somewhat confused. If I perform the following workflow:

1. Open slicer
2. Add two volumes (for now just one image each, 12 slices.)
3. Perform a B-Spline registration, registering the DTI image to the DCE image, creating a new volume for the output.
NB: At this point I am able to fade between the registered DTI image and the original DTI image, noting that an obvious transformation has occurred.

4. Save the scene, as well as the output volume (as nrrd).
5. Close slicer and re-open the scene file.

Then when I go back and compare the transformed image to the original, there is no difference. From here, if I re-calculate/re-apply the transformation, no change occurs in the image.

Also, once this condition occurs, nothing short of completely closing slicer will allow me to register and view the changes.

Is this known/intended behavior in Slicer? If so is there a way I can get around it? All I want to do is set up a scene with several sets of DTI/DCE images and their registered volumes, without having to re-calculate/re-sample them when  open it up again.

I'm using Slicer 3.4.1.0, WinXP SP3.


Thanks,

Kyzyl



--
Kyzyl Herzog

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Re: Saving Volumes

Andrey Fedorov
Not sure what's the problem, but couple of things to check:

1) sometimes Slicer would not notice that a volume/transform has
changed, and will not mark it as "Modified" when you are saving the
scene. In this case, your data will be lost on save. I think this was
reported as a bug, but I don't know if/when it was fixed (cannot find
it in mantis). So, when you are saving the scene, make sure that the
new volume is checked for saving

2) once things stop working, you should check the error log (small red
button in the right bottom corner). Please look if any errors are
reported there, and include them with your email.

3) try more recent build (3.4.2, or nightly), and let the list know if
the problem is reproduced.



On Sat, Feb 13, 2010 at 15:55, Kyzyl Herzog <[hidden email]> wrote:

> Anybody?
>
> On Thu, Feb 11, 2010 at 2:49 PM, Kyzyl Herzog <[hidden email]> wrote:
>>
>> Hello everyone,
>>
>> I'm experiencing some behavior in Slicer that has me somewhat confused. If
>> I perform the following workflow:
>>
>> 1. Open slicer
>> 2. Add two volumes (for now just one image each, 12 slices.)
>> 3. Perform a B-Spline registration, registering the DTI image to the DCE
>> image, creating a new volume for the output.
>> NB: At this point I am able to fade between the registered DTI image and
>> the original DTI image, noting that an obvious transformation has occurred.
>>
>> 4. Save the scene, as well as the output volume (as nrrd).
>> 5. Close slicer and re-open the scene file.
>>
>> Then when I go back and compare the transformed image to the original,
>> there is no difference. From here, if I re-calculate/re-apply the
>> transformation, no change occurs in the image.
>>
>> Also, once this condition occurs, nothing short of completely closing
>> slicer will allow me to register and view the changes.
>>
>> Is this known/intended behavior in Slicer? If so is there a way I can get
>> around it? All I want to do is set up a scene with several sets of DTI/DCE
>> images and their registered volumes, without having to
>> re-calculate/re-sample them when  open it up again.
>>
>> I'm using Slicer 3.4.1.0, WinXP SP3.
>>
>>
>> Thanks,
>>
>> Kyzyl
>
>
>
> --
> Kyzyl Herzog
>
> _______________________________________________
> 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: Saving Volumes

Andrey Fedorov
On Sat, Feb 13, 2010 at 16:11, Kyzyl Herzog <[hidden email]> wrote:
> Thanks for the feedback.
>
> 1. The volumes are checked.
> 2. There are no errors.
> 3. I'm on WinXP, which currently seems to have an issue with the latest
> build (unless that's been fixed in the last couple weeks). The program won't
> start on anything past 3.4.1 for me.

In this case, I would advice to include, if possible, the data
(anonymized), and log the detailed steps for reproducing the problem
on mantis as a bug (http://na-mic.org/Mantis/main_page.php).



> On Sat, Feb 13, 2010 at 1:08 PM, Andriy Fedorov <[hidden email]>
> wrote:
>>
>> Not sure what's the problem, but couple of things to check:
>>
>> 1) sometimes Slicer would not notice that a volume/transform has
>> changed, and will not mark it as "Modified" when you are saving the
>> scene. In this case, your data will be lost on save. I think this was
>> reported as a bug, but I don't know if/when it was fixed (cannot find
>> it in mantis). So, when you are saving the scene, make sure that the
>> new volume is checked for saving
>>
>> 2) once things stop working, you should check the error log (small red
>> button in the right bottom corner). Please look if any errors are
>> reported there, and include them with your email.
>>
>> 3) try more recent build (3.4.2, or nightly), and let the list know if
>> the problem is reproduced.
>>
>>
>>
>> On Sat, Feb 13, 2010 at 15:55, Kyzyl Herzog <[hidden email]> wrote:
>> > Anybody?
>> >
>> > On Thu, Feb 11, 2010 at 2:49 PM, Kyzyl Herzog <[hidden email]> wrote:
>> >>
>> >> Hello everyone,
>> >>
>> >> I'm experiencing some behavior in Slicer that has me somewhat confused.
>> >> If
>> >> I perform the following workflow:
>> >>
>> >> 1. Open slicer
>> >> 2. Add two volumes (for now just one image each, 12 slices.)
>> >> 3. Perform a B-Spline registration, registering the DTI image to the
>> >> DCE
>> >> image, creating a new volume for the output.
>> >> NB: At this point I am able to fade between the registered DTI image
>> >> and
>> >> the original DTI image, noting that an obvious transformation has
>> >> occurred.
>> >>
>> >> 4. Save the scene, as well as the output volume (as nrrd).
>> >> 5. Close slicer and re-open the scene file.
>> >>
>> >> Then when I go back and compare the transformed image to the original,
>> >> there is no difference. From here, if I re-calculate/re-apply the
>> >> transformation, no change occurs in the image.
>> >>
>> >> Also, once this condition occurs, nothing short of completely closing
>> >> slicer will allow me to register and view the changes.
>> >>
>> >> Is this known/intended behavior in Slicer? If so is there a way I can
>> >> get
>> >> around it? All I want to do is set up a scene with several sets of
>> >> DTI/DCE
>> >> images and their registered volumes, without having to
>> >> re-calculate/re-sample them when  open it up again.
>> >>
>> >> I'm using Slicer 3.4.1.0, WinXP SP3.
>> >>
>> >>
>> >> Thanks,
>> >>
>> >> Kyzyl
>> >
>> >
>> >
>> > --
>> > Kyzyl Herzog
>> >
>> > _______________________________________________
>> > 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
>> >
>
>
>
> --
> Kyzyl Herzog
>
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject