RepositioningMRIs - Meg Wiki

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Repositioning Structural MRIs

  • This repositioning should provide better normalisation of the of the individual structural MRIs to the Template stuctural, which is in MNI space. If the positioning of the individual MRI is far off the Template MRI, normalisation might fail (as Subject 9 in Demo). You can open and see the template from "/imaging/local/spm/spm5/canonical/single_subj_T1.nii" (below)

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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, it is just positioned to the centre of the image. 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)

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 ].

Since we want to make the anterior commissure 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.

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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]

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