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| Deletions are marked like this. | Additions are marked like this. |
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| After the anterior commissure is defined, it's coordinates relative to the existing origin are found in the "Crosshair Position" box, defined in mm, for the x,y,z axes. For the the structural below this corresponds to [0.0 38.5 16.1]. [ 1 ]. attachment:spm3cppt.png | After the anterior commissure is defined, it's coordinates relative to the existing origin are found in the "Crosshair Position" box, defined in mm, for the x,y,z axes. For the the structural below this corresponds to [0.0 38.5 16.1]. [ 1 ]. |
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| Since we want to make the anterior commisure the origin, the image needs to be "shifted" by these values. Hence in the "right {mm}" box [ 2 ] the value "0" is entered, in the "forward {mm}" the value "-38.5" [ 3 ] and in the "up {mm}" box the value "-16.1" [ 4 ]. attachment:spm4cppt.png Note that the sign of the values entered have the opposite sing than the ones in the Crosshair Position box. This is of course because the values in the Crosshair Position represent the differences between the current origin and the anterior commissure. Hence, after the anterior commissure is defined, the values entered in the "right", "forward" and "up" boxes should have the opposite sign than the ones in the Crosshair Position box. | attachment:spm3cppt.png Since we want to make the anterior commisure the origin, the image needs to be "shifted" by these values. Hence in the "right {mm}" box [ 2 ] the value "0" is entered, in the "forward {mm}" the value "-38.5" [ 3 ] and in the "up {mm}" box the value "-16.1" [ 4 ]. attachment:spm4cppt.png Note that the sign of the values entered have the opposite sing than the ones in the Crosshair Position box. This is of course because the values in the Crosshair Position represent the differences between the current origin and the anterior commissure. Hence, after the anterior commissure is defined, the values entered in the "right", "forward" and "up" boxes should have the opposite sign than the ones in the Crosshair Position box. |
Repositioning Structural MRIs
Repositioning structural MRIs to a common origin should help with the coregistration of the MEG/EEG data with the structural MRI. This repositioning provide better coregistration of the MEG/EEG fiducial coordinates obtained during Polhemus digitisation and the fiducial coordinates structural MRI.
Define the anterior commissure as the origin
When opening a structural image in SPM, the origin of the image is not registered to specific anatomical landmark. We use the anterior commissure as a landmark for the origin (also is the origin in the Template MRI used by SPM). The anterior commissure is an easily identifiable landmark (see http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures)
attachment:spm2cppt.png
Reorient images with anterior commissure as origin
After the anterior commissure is defined, it's coordinates relative to the existing origin are found in the "Crosshair Position" box, defined in mm, for the x,y,z axes. For the the structural below this corresponds to [0.0 38.5 16.1]. [ 1 ].
attachment:spm3cppt.png
Since we want to make the anterior commisure the origin, the image needs to be "shifted" by these values. Hence in the "right {mm}" box [ 2 ] the value "0" is entered, in the "forward {mm}" the value "-38.5" [ 3 ] and in the "up {mm}" box the value "-16.1" [ 4 ]. attachment:spm4cppt.png
Note that the sign of the values entered have the opposite sing than the ones in the Crosshair Position box. This is of course because the values in the Crosshair Position represent the differences between the current origin and the anterior commissure. Hence, after the anterior commissure is defined, the values entered in the "right", "forward" and "up" boxes should have the opposite sign than the ones in the Crosshair Position box.
Click the "Reorient Images" button [ 5 ] and select the file with the structural image [ 6 ], which will then be reoriented.
attachment:spm6cppt.png
To make sure that the process succeded, open the structural image again and click the the button underneath the "Crosshair Position" to move to the origin. If everything is correct the crosshairs will move to the anterior commisure and the xyz coordinates will be [0.0 0.0 0.0]
attachment:spm7cppt.png