[caret-users] Rotate volume image in Mac

Chen, Jessie Jessie.Chen at nyumc.org
Thu Nov 5 10:02:13 CST 2009

Hi Donna,

The AP-PC align worked beautifully, and it's very easy to do too. Thank you!


On 11/4/09 10:53 AM, "Donna Dierker" <donna at brainvis.wustl.edu> wrote:

Hi Jessie,

So is this a monkey (inferred from "the animal" below)?  I'll assume it is.

Depending on what you are doing with this data, and whether you will be
doing any type of group analysis, you might consider registering your
monkey to an existing volumetric atlas using FSL flirt or another affine
transform tool.  That would not only correct any orientation problems,
but also normalize for scale.  You could apply the inverse warp to your
surface to get it back in native space if needed.  If the tilt is too
severe, though, this may not work well.

In Caret, when you switch to Volume view, the toolbar changes, and
you'll see a H(XY) menu with the default axial view.  You can change
this to P (parasagittal), C (coronal), All, or Oblique.  That's one way
to rotate volume images, but that just affects what you see; it doesn't
affect the voxels written to the disk.

To correct a tilt in a way that saves a new, untilted volume, use
Volume: Edit Volume Attributes: AC-PC align.  Once you get it how you
want it, then go to Window: Transformation Matrix Editor and save the
resulting affine transform to a file, because you will need it to apply
to other data you want to map to the surface, or in order to apply the
inverse matrix to the surface to get it back to native later.  Also save
the resulting anatomical volume, of course.

I couldn't find a tutorial covering this, and I actually haven't used it
myself.  But I know Jason Hill used this feature on many baby brains, so
it does work.


On 11/03/2009 11:14 AM, Chen, Jessie wrote:
> Hi Donna,
> We are new to the Caret world. We are currently using Mac OS 10.4 to process the data. Since we didn't place the animal in stereotaxic during scanning, our images are bit tilted. Could you let us know how to freely rotate the volume images in Mac? Would that affect the cropping and 3D reconstruction down the line? Thanks a lot!
> Jessie
> ------------------------------
>    Jessie Chen, Ph.D.
>    Research Scientist
>    Dept. of Physiology and Neuroscience
>    New York University School of Medicine
>    New York, NY 10016
>    Tel: 212-263-2121
>    Fax: 212-263-6964
>    jessie.chen at nyumc.org
>    -------------------------------------------

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