[FieldTrip] change orientation of MRI or source plot

[Wu, Jia]

Jan-Mathijs,
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!
-jia

Input:
cfg=[];
cfg.method='spm';
target = 'template/T1.nii';
ft_volumerealign(cfg,mri,target);

Output:
the input is volume data with dimensions [256 256 256]
Warning: defaulting to  coordinate system
> In ft_volumerealign (line 238)
Input volume has coordinate system 'ctf'
Error using ft_convert_units (line 142)
cannot determine geometrical units

Error in ft_determine_coordsys (line 55)
data  = ft_convert_units(data);

Error in ft_convert_coordsys (line 59)
  obj = ft_determine_coordsys(obj, 'interactive', 'yes');

Error in ft_volumerealign (line 827)
      target = ft_convert_coordsys(target);


________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Schoffelen, J.M. (Jan Mathijs) [jan.schoffelen at donders.ru.nl]
Sent: Monday, September 28, 2015 3:20 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] change orientation of MRI or source plot

If you want the anatomical image to be displayed exactly the same as the template image you need to do the following 2 things:

-call ft_volumerealign, and impose a RAS coordinate system.
-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).

Best,
Jan-Mathijs



On Sep 25, 2015, at 4:46 PM, Wu, Jia <jia.wu at yale.edu<mailto:jia.wu at yale.edu>> wrote:

Hi,

I have a question about the orientation of MRI and source plot. I made the some comparison plot as below.
http://imgur.com/a/FoMAH<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=>

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.

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.

I'm wondering whether there is a way that I can change the orientation of the plot.

best,
-jia
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