Slicer3 misalignment

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Slicer3 misalignment

Marianna Jakab
Hello,

I have a bunch of MR datasets segmented with Slicer2. When I am loading the scene file into Slicer3 the segmented files are not recognized as volume.
I went back to Slicer2 and saved the segmented file as nrrd and a new scene file with a newly saved nrrd file. Then I have opened the new scene file in Slicer3.4 and 3.6, the greyscale image and the label files are being improperly aligned.

Any insight on this is nobly appreciated.

Thank you,

-Marianna
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Re: Slicer3 misalignment

pieper
Administrator
Hi Marianna -

Can you make a small sample dataset and scene file available for testing?

-Steve

On Aug/2/10 12:21 PM, Marianna Jakab wrote:

> Hello,
>
> I have a bunch of MR datasets segmented with Slicer2. When I am loading the scene file into Slicer3 the segmented files are not recognized as volume.
> I went back to Slicer2 and saved the segmented file as nrrd and a new scene file with a newly saved nrrd file. Then I have opened the new scene file in Slicer3.4 and 3.6, the greyscale image and the label files are being improperly aligned.
>
> Any insight on this is nobly appreciated.
>
> Thank you,
>
> -Marianna
> _______________________________________________
> 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: Slicer3 misalignment

Andrey Fedorov
Marianna,

As a temporary solution, you could probably set "Centered" flag in
"Add data" dialog for both grayscale and label volumes. Most likely
this will result in spatially aligned images.

AF



On Mon, Aug 2, 2010 at 16:49, Steve Pieper <[hidden email]> wrote:

> Hi Marianna -
>
> Can you make a small sample dataset and scene file available for testing?
>
> -Steve
>
> On Aug/2/10 12:21 PM, Marianna Jakab wrote:
>> Hello,
>>
>> I have a bunch of MR datasets segmented with Slicer2. When I am loading the scene file into Slicer3 the segmented files are not recognized as volume.
>> I went back to Slicer2 and saved the segmented file as nrrd and a new scene file with a newly saved nrrd file. Then I have opened the new scene file in Slicer3.4 and 3.6, the greyscale image and the label files are being improperly aligned.
>>
>> Any insight on this is nobly appreciated.
>>
>> Thank you,
>>
>> -Marianna
>> _______________________________________________
>> 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: Slicer3 misalignment

Marianna Jakab
Thank you, Andriy. Setting the "Centered" flag for both grayscale and label files worked. I have used "Add Volume" instead of "Add data".


-Marianna


Andriy Fedorov wrote:

> Marianna,
>
> As a temporary solution, you could probably set "Centered" flag in
> "Add data" dialog for both grayscale and label volumes. Most likely
> this will result in spatially aligned images.
>
> AF
>
>
>
> On Mon, Aug 2, 2010 at 16:49, Steve Pieper <[hidden email]> wrote:
>> Hi Marianna -
>>
>> Can you make a small sample dataset and scene file available for testing?
>>
>> -Steve
>>
>> On Aug/2/10 12:21 PM, Marianna Jakab wrote:
>>> Hello,
>>>
>>> I have a bunch of MR datasets segmented with Slicer2. When I am loading the scene file into Slicer3 the segmented files are not recognized as volume.
>>> I went back to Slicer2 and saved the segmented file as nrrd and a new scene file with a newly saved nrrd file. Then I have opened the new scene file in Slicer3.4 and 3.6, the greyscale image and the label files are being improperly aligned.
>>>
>>> Any insight on this is nobly appreciated.
>>>
>>> Thank you,
>>>
>>> -Marianna
>>> _______________________________________________
>>> 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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To unsubscribe: send email to [hidden email] with unsubscribe as the subject