Back to the main page.
Bug 1765 - standard_grid3d10mm does not fit well after non-linear warp
| Status | CLOSED FIXED |
| Reported | 2012-10-04 09:01:00 +0200 |
| Modified | 2013-05-09 08:31:03 +0200 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P3 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | 1930 |
| See also: |
Jan-Mathijs Schoffelen - 2012-10-04 09:01:14 +0200
Created attachment 336 template grid The standard_grid3d10mm fits more or less with the brain (although tight) at the top (see attachment). After non-linear warp to a single subject's brain the grid typically does not fit anymore at the top. Why would this be. -non-linear normalization does not care about the top, se leading to a less good fit. -non-linear normalization is bad altogether. -the non-linear transformation on the grid positions is incorrect (although the non-linear normalization may have been correct). -the template grid has been just too tight at the top.
Jan-Mathijs Schoffelen - 2012-10-04 09:01:39 +0200
Created attachment 337 non-linearly warped
Jan-Mathijs Schoffelen - 2012-10-04 09:11:10 +0200
Created attachment 338 8 mm grid
Jan-Mathijs Schoffelen - 2012-10-04 09:20:14 +0200
Created attachment 339 8 mm grid only linear warp
Jan-Mathijs Schoffelen - 2012-10-04 09:36:25 +0200
Created attachment 340 warped volume conductor model the white one is the template, the other one the warped subject volume conductor
Jan-Mathijs Schoffelen - 2012-10-08 12:06:58 +0200
Created attachment 341 standard mri with standard singleshell headmodel
Jan-Mathijs Schoffelen - 2012-10-08 12:15:04 +0200
Created attachment 342 standard mri with standard singelshell headmodel and warped individual headmodel
Jan-Mathijs Schoffelen - 2012-10-08 12:21:56 +0200
Created attachment 343 individual mri with warped standard singleshell headmodel and individual headmodel
Jan-Mathijs Schoffelen - 2012-10-08 12:29:40 +0200
after looking at it in a bit more detail, the conclusion here would be that the standard headmodel is wrapped tightly around the brain, whereas the individual headmodels are 'looser', and take into account the csf. For the 3D grid business it would seem reasonable to allow the 'looser' fit to be the definition of inside/outside, to allow for some interpolation edge. Discuss in FT-meeting, since this would entail building a new bunch of template grids etc, etc,...
Jan-Mathijs Schoffelen - 2013-03-07 09:18:10 +0100
bash-3.2$ svn add standard_sourcemodel* A (bin) standard_sourcemodel3d10mm.mat A (bin) standard_sourcemodel3d4mm.mat A (bin) standard_sourcemodel3d5mm.mat A (bin) standard_sourcemodel3d6mm.mat A (bin) standard_sourcemodel3d7point5mm.mat A (bin) standard_sourcemodel3d8mm.mat bash-3.2$ svn delete standard_grid* D standard_grid3d10mm.mat D standard_grid3d4mm.mat D standard_grid3d5mm.mat D standard_grid3d6mm.mat D standard_grid3d7point5mm.mat D standard_grid3d8mm.mat bash-3.2$ svn commit -m "enhancement - replaced tight template sourcemodels with sourcemodels with a looser fit" Deleting sourcemodel/standard_grid3d10mm.mat Deleting sourcemodel/standard_grid3d4mm.mat Deleting sourcemodel/standard_grid3d5mm.mat Deleting sourcemodel/standard_grid3d6mm.mat Deleting sourcemodel/standard_grid3d7point5mm.mat Deleting sourcemodel/standard_grid3d8mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d10mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d4mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d5mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d6mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d7point5mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d8mm.mat Transmitting file data ...... Committed revision 7600.
Jan-Mathijs Schoffelen - 2013-03-07 09:18:31 +0100
bash-3.2$ svn add standard_sourcemodel* A (bin) standard_sourcemodel3d10mm.mat A (bin) standard_sourcemodel3d4mm.mat A (bin) standard_sourcemodel3d5mm.mat A (bin) standard_sourcemodel3d6mm.mat A (bin) standard_sourcemodel3d7point5mm.mat A (bin) standard_sourcemodel3d8mm.mat bash-3.2$ svn delete standard_grid* D standard_grid3d10mm.mat D standard_grid3d4mm.mat D standard_grid3d5mm.mat D standard_grid3d6mm.mat D standard_grid3d7point5mm.mat D standard_grid3d8mm.mat bash-3.2$ svn commit -m "enhancement - replaced tight template sourcemodels with sourcemodels with a looser fit" Deleting sourcemodel/standard_grid3d10mm.mat Deleting sourcemodel/standard_grid3d4mm.mat Deleting sourcemodel/standard_grid3d5mm.mat Deleting sourcemodel/standard_grid3d6mm.mat Deleting sourcemodel/standard_grid3d7point5mm.mat Deleting sourcemodel/standard_grid3d8mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d10mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d4mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d5mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d6mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d7point5mm.mat Adding (bin) sourcemodel/standard_sourcemodel3d8mm.mat Transmitting file data ...... Committed revision 7600.