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Bug 1314 - consider incorporating MNI source grids into ft_prepare_sourcemodel
| Status | CLOSED FIXED |
| Reported | 2012-02-07 17:43:00 +0100 |
| Modified | 2012-07-07 20:25:07 +0200 |
| Product: | FieldTrip |
| Component: | forward |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P3 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | 1122 |
| Blocks: | |
| See also: |
Robert Oostenveld - 2012-02-07 17:43:35 +0100
tbd
Johanna - 2012-02-08 10:02:03 +0100
Not sure exactly the plan or what's needed/required/assumed, but maybe nut_makeMNIvoi can help with ideas? It takes a requested voxel spacing, assuming the subject's MRI has been normalised to MNI, and creates the grid in MNI coords, inside the bounds defined by the MNI brain and *_sn.mat mapping.
Robert Oostenveld - 2012-02-08 10:31:17 +0100
(In reply to comment #1) something along these lines was indeed what I was thinking of, and something like http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space The thought was inspired by a discussion with Vladimir, in which we looked at the SPM source reconstruction pipeline. SPM makes a lot of use of templates and warps them back and forth. We actually do the same, but not in a user-friendly way. My idea is that instead of a long recipe as in the example script on the wiki, we would enhance the ft_prepare_sourcemodel function to allow for a short recipe that involves - ft_normalisevolume - ft_prepare_sourcemodel
Johanna - 2012-02-08 10:49:26 +0100
Created attachment 226 Nutmeg file to create MNI voi I've attached the file in case it helps ideas. It needs some sub-functions, let me know if I should post those too.
Jan-Mathijs Schoffelen - 2012-02-10 10:37:39 +0100
first implementation in revision 5270 use as cfg = []; cfg.mri = ... cfg.grid.warpmni = 'yes'; cfg.grid.resolution = 10; grid=ft_sourcemodel(cfg); TO DO: update documentation, and check the template grids
Jan-Mathijs Schoffelen - 2012-04-11 10:31:12 +0200
implemented nonlinear warping in revision 5604. To do: update documentation