Step 3: Coregister anatomical image to the mean functional image

Because the subject may have moved slightly between collection of the structural image and the functional images, it is necessary to coregister the structural image to the mean functional image produced in the realignment stage above.

Click on the “COREGISTER” button

Select Corgister: Estimate and Reslice

For the Reference Image use the mean image created during realignment. It will be found in session 1 and is named meanaV001.img.

For Source Image use the structural image you obtained during scanning.

For Other images do not enter more images.

For Reslice Options -> masking select Don’t mask images.

If any images are selected as “other”, the tranformation parameters esimated to coregister the object to the taget image will also be applied to the “other” images. This step will find the transformation that maps the anatomical inplane image into the space of the functional images (as defined by the mean image). A new image, rS.img will be created.

The results from this stage are displayed in the SPM Graphics window. At the bottom of this window, the target image is displayed on the left (in our case, the mean functional) and the source image is displayed on the right (in our case, the transformed coregistered structural). To check that the coregistration went well, click on the edges of the brain to see whether they correspond to the edges of the other brain. (You can navigate the brain image, by clicking in different locations on any of the cross-sections.)

You can also check the coregistration between these (or any other) images at a later stage, by clicking the “Check Reg” button in SPM, and selecting the images to examine.

If the coregistration did not work well, it may be necessary to use skull-stripping routines, to remove the skull from the functional image and MRIcro to remove any traces of skull from the mean functional image, before redoing the registration step.