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| Deletions are marked like this. | Additions are marked like this. |
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| Here, the !FreeSurfer data is referred to as 'fs_brain' although any FreeSurfer subject could be used. | Here, the !FreeSurfer data is referred to as 'fs_brain' although any !FreeSurfer subject could be used. |
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| * Within the fs_brain/mri directory is brain.mgz that needs to be converted to an analyse image using !FreeSurfers mri_convert function: . e.g. mri_convert $SUBJECTS_DIR/fs_brain/mri/brain.mgz brain.img This creates brain.img which is saved in the current directory. * Within SPM, use the coregister: Estimate option with the !FreeSurfer brain.img at the reference and an SPM MNI brain image as the source (you may want to use a local copy rather than the spm version). |
* Within the fs_brain/mri directory is brain.mgz that needs to be converted to an analyse image using !FreeSurfer's mri_convert function: . e.g. mri_convert $SUBJECTS_DIR/fs_brain/mri/brain.mgz brain.img This creates brain.img which is saved in the current directory. * Within SPM, use the "Coregister:Estimate" option with the !FreeSurfer brain.img as the reference and an SPM MNI brain image as the source (you may want to use a local copy rather than the spm version). |
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| * Then compare how well the FreeSurfer and SPM images are registered using the COMPARE button to flip between the images. If ok, click save, and the registration file (register.dat) will save in the current directory. | * Then compare how well the !FreeSurfer and SPM images are registered using the COMPARE button to flip between the images. If ok, click save, and the registration file (register.dat) will save in the current directory. |
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| Note: With this approach, the correspondence between the SPM anatomy and the !FreeSurfer anatomy will only be as good as the co-registration. For increased anatomical correspondence between the SPM location and that on the inflated cortex, you may want to use an MNI brain as input into FreeSurfer's recon procedures creating an inflated version of the MNI brain. | Note: With this approach, the correspondence between the SPM anatomy and the !FreeSurfer anatomy will only be as good as the co-registration. For increased anatomical correspondence between the SPM location and that on the inflated cortex, you may want to use an MNI brain as input into !FreeSurfer's recon procedures creating an inflated version of the MNI brain. |
Displaying SPM images with FreeSurfer
Here it is outlined how to display your SPM results (or any analyze image) on the cortical surface provided with FreeSurfer.
Here, the FreeSurfer data is referred to as 'fs_brain' although any FreeSurfer subject could be used.
Within the fs_brain/mri directory is brain.mgz that needs to be converted to an analyse image using FreeSurfer's mri_convert function:
- e.g. mri_convert $SUBJECTS_DIR/fs_brain/mri/brain.mgz brain.img
Within SPM, use the "Coregister:Estimate" option with the FreeSurfer brain.img as the reference and an SPM MNI brain image as the source (you may want to use a local copy rather than the spm version).
The FreeSurfer program tkregister2 is then used to create a registration file that maps between the two spaces, where the SPM_file.img is the SPM template brain.
- tkregister2 --s fs_brain --mov SPM_file.img --regheader --reg register.dat --surf orig
Then compare how well the FreeSurfer and SPM images are registered using the COMPARE button to flip between the images. If ok, click save, and the registration file (register.dat) will save in the current directory.
- To view functional data on an inflated surface, it can be loaded as an overlay in tksurfer using the register.dat as the registration file.
Note: With this approach, the correspondence between the SPM anatomy and the FreeSurfer anatomy will only be as good as the co-registration. For increased anatomical correspondence between the SPM location and that on the inflated cortex, you may want to use an MNI brain as input into FreeSurfer's recon procedures creating an inflated version of the MNI brain.
More info on the!FreeSurfer wiki:
* http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting
* http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SpmFreeSurfer