[FieldTrip] ft_volumerealign

[Markus Butz]

Dear list

when running ft_volumerealign with the spm template MRI in the interactive mode, I get something like: 


============================================================================
voxel 838065, indices [46 54 85], location [0.0 -20.0 96.0] mm
nas_voxel = [46.000000 104.000000 11.000000], nas_head = [0.000000 80.000000 -52.000000]
lpa_voxel = [5.000000 54.000000 11.000000], lpa_head = [82.000000 -20.000000 -52.000000]
rpa_voxel = [85.000000 54.000000 11.000000], rpa_head = [-78.000000 -20.000000 -52.000000]
xzpoint_voxel = [46.000000 54.000000 85.000000], xzpoint_head = [0.000000 -20.000000 96.000000]
the call to "ft_volumerealign" took 136 seconds and an estimated 39 MB


Now I would like to rerun it in the fiducial mode, using the above information.
According to help, I need to do this:


For realigning to the fiducials, you should specify the position of the fiducials in voxel indices.
    cfg.fiducial.nas  = [i j k], position of nasion
    cfg.fiducial.lpa  = [i j k], position of LPA
    cfg.fiducial.rpa  = [i j k], position of RPA



I used the voxel indices (code below), but ended up with the MRI upside-down (see attached picture).
Trying the landmark mode was also without success.


Am I doing something silly here?



Thanks in advance
Markus




% Load SPM8 T1 template 


 template     = '/Documents/MATLAB/spm8/templates/T1.nii';


 template_mri = ft_read_mri(template);


 disp(template_mri)


 


 % 2. Realign the coordinate system


 cfg                = []; 


 cfg.method         = 'fiducial'; % 'interactive';


 cfg.fiducial.nas   = [46 104 11];


 cfg.fiducial.lpa   = [5 54 11];


 cfg.fiducial.rpa   = [85 54 12];


 cfg.fiducial.zpoint= [46 54 85];


 cfg.coordsys       = 'ctf';


 template_mri_realigned  = ft_volumerealign(cfg, template_mri);






 


 % 3. Check the coordinate system


 cfg                     = [];


 cfg.interactive         = 'yes';


 template_mri_checked    = ft_determine_coordsys(template_mri_realigned);


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