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help > RE: Surf Ice vs SPM rendering - different outputs
Nov 1, 2016 01:11 PM | Chris Rorden
RE: Surf Ice vs SPM rendering - different outputs
Lydia-
The NIfTI files saved by SPM are on discrete voxel grid, while Surf Ice interpolates these values to a 2D mesh. In other words, there is not a perfect one-to-one correspondence with each NIfTI voxel and each mesh vertex. I have a couple thoughts on this:
1.) You will probably get a stronger correspondence between SPM and MRIcroGL (which is a volume renderer based on voxels) than between SPM and Surf Ice.
2.) The depth of your surface mesh also plays a role, for example the surface of the the mesh mni152_2009.mz3 is much less eroded than BrainMesh_ICBM152.mz3, so the latter will probably catch signal that is not precisely on the surface.
3.) I would strongly recommend that for both Surf Ice and MRIcroGL you you load an UNTHRESHOLDED statistical map, and then apply your numerical threshold. If you use SPM to save a THRESHOLDED image, then you are artificially surrounding the activity with zero values, and this will make the interpolated activity look less significant and smaller than it is in fact (due to smoothing, voxels near clusters that survive thresholding tend to have values close to the threshold value, and far from zero). For FSL users, you would want to load your "zstat1.nii.gz" as an overlay, rather than the "thresh_zstat1.nii.gz" and then apply your statistical threshold.
The NIfTI files saved by SPM are on discrete voxel grid, while Surf Ice interpolates these values to a 2D mesh. In other words, there is not a perfect one-to-one correspondence with each NIfTI voxel and each mesh vertex. I have a couple thoughts on this:
1.) You will probably get a stronger correspondence between SPM and MRIcroGL (which is a volume renderer based on voxels) than between SPM and Surf Ice.
2.) The depth of your surface mesh also plays a role, for example the surface of the the mesh mni152_2009.mz3 is much less eroded than BrainMesh_ICBM152.mz3, so the latter will probably catch signal that is not precisely on the surface.
3.) I would strongly recommend that for both Surf Ice and MRIcroGL you you load an UNTHRESHOLDED statistical map, and then apply your numerical threshold. If you use SPM to save a THRESHOLDED image, then you are artificially surrounding the activity with zero values, and this will make the interpolated activity look less significant and smaller than it is in fact (due to smoothing, voxels near clusters that survive thresholding tend to have values close to the threshold value, and far from zero). For FSL users, you would want to load your "zstat1.nii.gz" as an overlay, rather than the "thresh_zstat1.nii.gz" and then apply your statistical threshold.
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Title | Author | Date |
---|---|---|
Lydia Vinals | Oct 28, 2016 | |
Chris Rorden | Nov 1, 2016 | |