Orthogonal Views Bug/Feature Request

[MRG]

Hi,

System: ImageJ 1.45s; Java 1.6.0_20 (64-bit); Windows 7 64-bit; 4Gb RAM
allocated

I'm trying to reformat axial CT head scans into coronal and sagittal views
to assist with interpretation.  I've opened the DICOM files as an image
stack (caudal to cranial).  Trouble is, the Orthogonal Views command gives
me the coronal  (XZ) images upside-down and sagittals (YZ) rotated 90
degrees clockwise.  I can see why this is the default behaviour and I am
able to correct the coronals with the "Flip Vertically" function.  However,
though applying the "Rotate 90 Degrees Left" transform to the sagittals
initially appears to work, when I then try to scroll the images the sagittal
stack immediately reverts to the original rotated format.  

Is it possible to fix the problem with applying a rotation to the sagittals?
I don't expect the Orthogonal Views function to change its default behaviour
or have options in terms of how it presents the reformatted images. It is
easy for me to write a macro that reorients the coronals and sagittals to
how I need as long as the necessary transforms can be applied to the
respective image stacks.

Thanks

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[tao sun]

Hello,

You may want to try TransformJ.

Regards,
Sun Tao

2012/4/5 [hidden email] <[hidden email]>

> Hi,
>
> System: ImageJ 1.45s; Java 1.6.0_20 (64-bit); Windows 7 64-bit; 4Gb RAM
> allocated
>
> I'm trying to reformat axial CT head scans into coronal and sagittal views
> to assist with interpretation.  I've opened the DICOM files as an image
> stack (caudal to cranial).  Trouble is, the Orthogonal Views command gives
> me the coronal  (XZ) images upside-down and sagittals (YZ) rotated 90
> degrees clockwise.  I can see why this is the default behaviour and I am
> able to correct the coronals with the "Flip Vertically" function.  However,
> though applying the "Rotate 90 Degrees Left" transform to the sagittals
> initially appears to work, when I then try to scroll the images the
> sagittal
> stack immediately reverts to the original rotated format.
>
> Is it possible to fix the problem with applying a rotation to the
> sagittals?
> I don't expect the Orthogonal Views function to change its default
> behaviour
> or have options in terms of how it presents the reformatted images. It is
> easy for me to write a macro that reorients the coronals and sagittals to
> how I need as long as the necessary transforms can be applied to the
> respective image stacks.
>
> Thanks
>
> --
> View this message in context:
> http://imagej.1557.n6.nabble.com/Orthogonal-Views-Bug-Feature-Request-tp4689096p4689096.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Apr 5, 2012, at 7:14 AM, [hidden email] wrote:

> Hi,
>
> System: ImageJ 1.45s; Java 1.6.0_20 (64-bit); Windows 7 64-bit; 4Gb RAM
> allocated
>
> I'm trying to reformat axial CT head scans into coronal and sagittal views
> to assist with interpretation.  I've opened the DICOM files as an image
> stack (caudal to cranial).  Trouble is, the Orthogonal Views command gives
> me the coronal  (XZ) images upside-down and sagittals (YZ) rotated 90
> degrees clockwise.  I can see why this is the default behaviour and I am
> able to correct the coronals with the "Flip Vertically" function.  However,
> though applying the "Rotate 90 Degrees Left" transform to the sagittals
> initially appears to work, when I then try to scroll the images the sagittal
> stack immediately reverts to the original rotated format.  
>
> Is it possible to fix the problem with applying a rotation to the sagittals?
> I don't expect the Orthogonal Views function to change its default behaviour
> or have options in terms of how it presents the reformatted images. It is
> easy for me to write a macro that reorients the coronals and sagittals to
> how I need as long as the necessary transforms can be applied to the
> respective image stacks.

Try enabling "Rotate YZ" and "Flip XZ" in Edit>Options>DICOM.

-wayne