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<div style="direction: ltr;font-family: Tahoma;color: #000000;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 <br>
> In ft_volumerealign (line 238) <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>
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<div style="direction: ltr;" id="divRpF676864"><font face="Tahoma" color="#000000" size="2"><b>From:</b> fieldtrip-bounces@science.ru.nl [fieldtrip-bounces@science.ru.nl] on behalf of Schoffelen, J.M. (Jan Mathijs) [jan.schoffelen@donders.ru.nl]<br>
<b>Sent:</b> Monday, September 28, 2015 3:20 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] change orientation of MRI or source plot<br>
</font><br>
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<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>
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<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>
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<div>Best,</div>
<div>Jan-Mathijs</div>
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<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>
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<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>
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