📄 mri_orientation_notes.html

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<h1>MRI Orientation Notes</h1>

<p>The mri_toolbox download at 
<a href="http://eeg.sf.net">http://eeg.sf.net</a>
contains matlab code that employs the orient header field to read and 
orthotransform ANALYZE volumes (see the avw* functions).  In this code 
(ie, avw_img_read.m) there is complete documentation of the XYZ directions 
for all 6 orthogonal orientations defined by ANALYZE in the avw.hdr.hist.orient 
field, namely:<br>

<ul>
<li>          0,  transverse unflipped (LAS*)</li> 
<li>          1,  coronal unflipped (LA*S)</li> 
<li>          2,  sagittal unflipped (L*AS)</li> 
<li>          3,  transverse flipped (LPS*)</li> 
<li>          4,  coronal flipped (LA*I)</li> 
<li>          5,  sagittal flipped (L*AI)</li>
</ul>
where * follows the slice dimension and letters indicate +XYZ
orientations (L left, R right, A anterior, P posterior,
I inferior, &amp; S superior). These values can be used in avw_img_read or
avw_img_write to read/write the corresponding orientation correctly.</p>

<p>The default ANALYZE orientation is LAS (radiological orientation):<br> 
<ul>
<li>+X is <u>L</u>eft</li> 
<li>+Y is <u>A</u>nterior</li> 
<li>+Z is <u>S</u>uperior</li>
</ul>
This corresponds to: avw.hdr.hist.orient = 0, transverse unflipped.</p>

<p>The neurological convention is RAS (only the direction of X is swapped):<br>
<ul>
<li>+X is <u>R</u>ight</li> 
<li>+Y is <u>A</u>nterior</li> 
<li>+Z is <u>S</u>uperior</li>
</ul>
This is also the 'Talairach' and MNI template coordinate system.

For more details on Talairach space and normalization with the MNI templates,
see the notes from Chris Rorden and Matthew Brett:<br>
<a href="http://www.mricro.com/anatomy/">
         http://www.mricro.com/anatomy/</a>,<br>
<a href="http://www.mrc-cbu.cam.ac.uk/Imaging/brodmann_areas.html">
         http://www.mrc-cbu.cam.ac.uk/Imaging/brodmann_areas.html</a>,<br>
<a href="http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html">
         http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html</a>, where the latter
matlab functions are included in this toolbox.<br>
The standard analyze format does not support the neurological orientation in
either the hdr.hist.orient field or the .img file data order.  You can use 
avw_flip to obtain this, but it is a violation of the Analyze file
format.</p>

<p>This toolbox will try to load an Analyze volume (actually any .img file)
as an LAS volume, so long as the avw.hdr.hist.orient field is set correctly.  
Thus, the avw_view function should always present the volume in LAS (radiological) 
orientation (a GUI control allows easy L/R flipping for viewing purposes).  If 
you need to, you can use avw_flip to orthoflip any dimension, although this 
could easily invalidate the Analyze coordinate system (NOT recommended).</p>

<p>The avw.hdr.hist.orient field is "optional" and not all software will read
or write it correctly.  For example,
<a href="http://www.fil.ion.ucl.ac.uk/spm/">SPM</a> ignores it and 
<a href="http://www.sensor.com">MEDx</a> sets an unused header field.</p>

<p>The flipped orientations (orient values 3-5) are only defined in
Analyze to support a movie animation.  The flipping is not done in the slice
direction, but rather in the dimension that suits raster graphics.  The flipping
has NO relationship to the actual orientation of the volume, only to how the 
data is handled during graphics processes.  Thus, orient values 3-5 are NOT 
recommended. For example, for a transverse LAS volume, the orient=3 option 
flips to the anterior-posterior direction (LPS), which does not provide for 
saving RAS volumes.  Nevertheless, this toolbox will attempt to handle the 
flipped Analyze volumes correctly.</p>

<p>If your not sure what the orientation of a volume is, it is near impossible
to differentiate LAS from RAS without landmarks in the image.  A useful tool is
the flip L/R control in avw_view.  It will allow you to quickly flip left/right
to find visual cues that differentiate these two orientations.  Often the 
ventricles provide good asymmetry indicators.  Some high resolution T1 
anatomical data I have worked with was acquired with a small pinpoint 
artifact in the central voxel of the left most slice of the volume 
(what a great idea! except when it comes to intensity normalisation!).  It's
also possible to use radiological markers (a preferable method, perhaps, as it
should avoid the intensity artifact when normalising or correcting Bo field 
distortions).  If that information is not available to you, but you have 
the original scanner files, you can use your favourite software or some free
offerrings:
<a href="http://www.mricro.com/">http://www.mricro.com/</a> or 
<a href="http://xmedcon.sourceforge.net">http://xmedcon.sourceforge.net</a> 
to read the original scanner volume headers, which usually contain useful 
orientation information, if you can interpret it (maybe speak to your 
radiographer).  You might then use MRIcro or Xmedcon to convert
the original data to ANALYZE, in a specific orientation.  Keep careful track
of the orientation during this conversion, especially left/right.  Also 
consider acquisition of a small phantom volume, containing LAS orientation 
markers, in the sequence you use for your subject data.  You can then process 
that volume through all the stages of your analyses to confirm the final 
orientation.</p>

<p>When working with format conversions, consider these 
<a href="MJenkinson_coordtransforms.pdf">enlightening notes</a> from
Mark Jenkinson!</p>

<p>All the best getting it right.  MRI volume orientation has been a problem
for me, prompting development of the MRI_toolbox.  After better understanding 
how it works, the anxiety dissipates ;-) (although never really leaves you at 
peace). It's frustrating that our visuo-spatial intelligence for 3D object 
orientation virtually goes out the window when looking at ortho slices!  In 
reality, we know this is a simple problem, yet the ortho views are unyielding!</p>


<h3>Further comments on -X pixdim and neurological convention,
 with an illustration and some issues to clarify</h3>

<p>Just to get down to basics, imagine a 2D axial slice through the AC, 
viewed with the nose at the top.
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