how to change orientation

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how to change orientation

Akiko U
Dear 3Dslicer-users,

I converted .ima format files to .dcm file through a software called
MedCon. I don't know whether it happened due to that or not,

but orientations of saggital and coronal images  were somewhat upside down.

could you tell me how to fix it?

thank you,

akiko
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Re: how to change orientation

swallace
Looking at the documentation, that software ignored file orientation,
hence the issue.

Try Orient Images module:

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



Stuart

> Dear 3Dslicer-users,
>
> I converted .ima format files to .dcm file through a software called
> MedCon. I don't know whether it happened due to that or not,
>
> but orientations of saggital and coronal images  were somewhat upside
> down.
>
> could you tell me how to fix it?
>
> thank you,
>
> akiko
> _______________________________________________
> 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: how to change orientation

pieper
Administrator
Hi Akiko -

I agree with Stuart, the problem probably was with the MedCon software.

As another option to fix it, you can put the volume in a transform and
flip the axes by editing the diagonal elements.  Then you can 'harden'
the transform and re-export the dicom files so they will be correct when
loaded in slicer and other packages.  Be careful with the left-right
flip since that can be difficult to verify by visual inspection for
things like brain images.

-Steve

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

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

http://www.slicer.org/slicerWiki/index.php/Coordinate_systems



On Sep/7/10 9:29 AM, [hidden email] wrote:

> Looking at the documentation, that software ignored file orientation,
> hence the issue.
>
> Try Orient Images module:
>
> http://www.slicer.org/slicerWiki/index.php/Modules:OrientImages-Documentation-3.6
>
>
>
> Stuart
>
>> Dear 3Dslicer-users,
>>
>> I converted .ima format files to .dcm file through a software called
>> MedCon. I don't know whether it happened due to that or not,
>>
>> but orientations of saggital and coronal images  were somewhat upside
>> down.
>>
>> could you tell me how to fix it?
>>
>> thank you,
>>
>> akiko
>> _______________________________________________
>> 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: how to change orientation

Dominik Meier
I agree with Steve. "OrientImages" will reslice but won't change how images appear when reloaded.

You can find a similar example of orientation fixes in the Registration Case Library #14


The associated PowerPoint Tutorial contains slides explaining orientation changes. 

Dominik



On Sep 7, 2010, at 9:49 AM, Steve Pieper wrote:

Hi Akiko -

I agree with Stuart, the problem probably was with the MedCon software.

As another option to fix it, you can put the volume in a transform and 
flip the axes by editing the diagonal elements.  Then you can 'harden' 
the transform and re-export the dicom files so they will be correct when 
loaded in slicer and other packages.  Be careful with the left-right 
flip since that can be difficult to verify by visual inspection for 
things like brain images.

-Steve






On Sep/7/10 9:29 AM, [hidden email] wrote:
Looking at the documentation, that software ignored file orientation,
hence the issue.

Try Orient Images module:




Stuart

Dear 3Dslicer-users,

I converted .ima format files to .dcm file through a software called
MedCon. I don't know whether it happened due to that or not,

but orientations of saggital and coronal images  were somewhat upside
down.

could you tell me how to fix it?

thank you,

akiko
_______________________________________________
slicer-users mailing list
To unsubscribe: send email to
[hidden email] with unsubscribe as the
subject




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_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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