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Hi Jia,
<div><br>
</div>
<div>RAS is just shorthand for a coordinate system that uses a convention where the X,Y and Z axes of the coordinate system (relative to a meaningful object, in our case: the brain) is pointing to the right, anterior and superior respectively. In order to define
the anatomical image in a RAS coordinate system, you should call ft_volumerealign with one of the two following inputs:</div>
<div><br>
</div>
<div>case 1):</div>
<div><br>
</div>
<div>cfg = [];</div>
<div>cfg.method = ‘interactive’;</div>
<div>cfg.coordsys = ‘neuromag’;</div>
<div>mri = ft_volumerealign(cfg, mri);</div>
<div><br>
</div>
<div>then you can click around in the volume, and define the lpa,rpa and nasion fiducials (with the l,r, and n keys)</div>
<div><br>
</div>
<div>case 2):</div>
<div><br>
</div>
<div>cfg = [];</div>
<div>cfg.method = ‘interactive’;</div>
<div>mri = ft_volumerealign(cfg, mri);</div>
<div><br>
</div>
<div>if you now click around, you can define the anterior commissure, the posterior commissure, and a point along the positive z-axis, and a point along the positive x-axis (with, respectively, the keys a, p, z and r).</div>
<div><br>
</div>
<div>Either way, you’ll result in an anatomical image that has an RAS-coordinate system (yet both with different origins, as defined and described in the documentation that Tzvetan pointed you to), and I assume that you are after the ‘SPM’-based coordinate
system, which uses the anatomical landmarks (anterior and posterior commissures to define the origin and the direction of the y-axis).</div>
<div><br>
</div>
<div>Next, you can call ft_volumereslice to align the cardinal voxel axes to the axes of your RAS coordinate system.</div>
<div><br>
</div>
<div>As an explanatory note, CTF uses a so-called ALS coordinate system, wher the X-axis points to anterior, the Y axis to the left, and the Z-axis to the top of the head. On the screen, after a ft_volumereslice, this gives a picture with a 90 degree rotation
around the z-axis, because the physical interpretation of the x and y axes are different (‘RA' versus ‘AL’).</div>
<div><br>
</div>
<div>I realize that there is also a case 3 that you can do, which does not require an interactive step:</div>
<div><br>
</div>
<div>case 3):</div>
<div><br>
</div>
<div>cfg = [];</div>
<div>cfg.nonlinear = ‘no’;</div>
<div>mrin = ft_volumenormalise(cfg, mri);</div>
<div>mrir = ft_volumereslice([],mrin);</div>
<div><br>
</div>
<div>If you call ft_volumenormalise with cfg.nonlinear = ‘no’, the affine transformation is estimated that goes from voxel space to a RAS coordinate system with the origin in the anterior commissure (approximately). This should be more or less equivalent to
case 2) above.</div>
<div><br>
</div>
<div>Best,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On Sep 28, 2015, at 4:57 PM, Wu, Jia <<a href="mailto:jia.wu@yale.edu">jia.wu@yale.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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<div style="direction: ltr; font-family: Tahoma; font-size: 10pt;">Jan-Mathijs,<br>
Thank you very much for the note. I'm not sure how to impose a RAS coordinate system. I tried the following code and got an error. If you have a quick moment do you mind pointing me to the right direction? Thank you so much!<br>
-jia<br>
<br>
Input:<br>
cfg=[];<br>
cfg.method='spm';<br>
target = 'template/T1.nii';<br>
ft_volumerealign(cfg,mri,target);<br>
<br>
Output:<br>
the input is volume data with dimensions [256 256 256]<br>
Warning: defaulting to coordinate system<span class="Apple-converted-space"> </span><br>
> In ft_volumerealign (line 238)<span class="Apple-converted-space"> </span><br>
Input volume has coordinate system 'ctf'<br>
Error using ft_convert_units (line 142)<br>
cannot determine geometrical units<br>
<br>
Error in ft_determine_coordsys (line 55)<br>
data = ft_convert_units(data);<br>
<br>
Error in ft_convert_coordsys (line 59)<br>
obj = ft_determine_coordsys(obj, 'interactive', 'yes');<br>
<br>
Error in ft_volumerealign (line 827)<br>
target = ft_convert_coordsys(target);<br>
<br>
<br>
<div style="font-family: 'Times New Roman'; font-size: 16px;">
<hr tabindex="-1">
<div id="divRpF676864" style="direction: ltr;"><font face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a><span class="Apple-converted-space"> </span>[<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>]
on behalf of Schoffelen, J.M. (Jan Mathijs) [<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>]<br>
<b>Sent:</b><span class="Apple-converted-space"> </span>Monday, September 28, 2015 3:20 AM<br>
<b>To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list<br>
<b>Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] change orientation of MRI or source plot<br>
</font><br>
</div>
<div></div>
<div>If you want the anatomical image to be displayed exactly the same as the template image you need to do the following 2 things:
<div><br>
</div>
<div>-call ft_volumerealign, and impose a RAS coordinate system.</div>
<div>-call ft_volumereslice, to align the i/j/k voxel axes with the x/y/z coordinate axes (which in the previous step were constructed to be RAS).</div>
<div><br>
</div>
<div>Best,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On Sep 25, 2015, at 4:46 PM, Wu, Jia <<a href="mailto:jia.wu@yale.edu" target="_blank">jia.wu@yale.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="font-family: Calibri; font-size: 15px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px;">
<div style="direction: ltr; font-family: Tahoma; font-size: 10pt;">Hi,<br>
<br>
I have a question about the orientation of MRI and source plot. I made the some comparison plot as below.<br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FoMAH&d=AwMFAw&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=9ehCplyXHP0-m9ayYv1FOg&m=zO_2mE8ZYtGGWpMORuQp1nczgv9nyCvAMO2hB87pvOE&s=_D8VLWPcGCa0JhIGjF07gXmcf7jXMhXdzO2ZcpuMrwM&e=" target="_blank">http://imgur.com/a/FoMAH</a><br>
<br>
The top image is a plot of the T1template, which follows the convention that the top left is coronal, top right is sagittal and the bottom left is axial.<span class="Apple-converted-space"> </span><br>
<br>
The bottom image is from Subject01.mri downloaded from the fieldtrip server and applied volumeslice. (Without using volumeslice the orientation is not correct either). The coronal and sagittal views were switched.<span class="Apple-converted-space"> </span><br>
<br>
I'm wondering whether there is a way that I can change the orientation of the plot.<br>
<br>
best,<br>
-jia<br>
</div>
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