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Bug 1590 - simbio fem modeling should be documented

Reported 2012-07-03 15:27:00 +0200
Modified 2016-01-04 15:59:32 +0100
Product: FieldTrip
Component: forward
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P3 normal
Assigned to: Simon
Depends on: 1820
See also:

Robert Oostenveld - 2012-07-03 15:27:33 +0200

At the moment the documentation is % FT_HEADMODEL_SIMBIO reads a volume conduction model from a Vista *.v file % % Use as % vol = ft_headmodel_fem_simbio(seg) % % See also FT_PREPARE_VOL_SENS, FT_COMPUTE_LEADFIELD, TEST_HEADMODEL_SIMBIO which mentions no options at all, whereas it uses a long list of options: wfmethod = ft_getopt(varargin, 'wfmethod', 'cubes'); % wireframe method (default: cubes) transform = ft_getopt(varargin, 'transform', []); % contains the tr. matrix from voxels to head coordinates unit = ft_getopt(varargin, 'unit', 'mm'); % contains the units of the transformation matrix (mm, cm, ...) tissue = ft_getopt(varargin, 'tissue', []); % contains the labels of the tissues tissueval = ft_getopt(varargin, 'tissueval', []); % contains the tissue values (an integer for each compartment) tissuecond = ft_getopt(varargin, 'tissuecond', []); % contains the tissue conductivities tissueweight = ft_getopt(varargin, 'tissueweight', ones(1,numel(tissueval))); % contains the weigths for vgrid (how dense the wireframe of each tissue conpartment should deepelec = istrue(ft_getopt(varargin, 'deepelec', 'no')); % used in the case of deep voxel solution % bnd = ft_getopt(varargin, 'bnd', []); % used in the case the solution has to be calculated on a triangulated surface (typically the scalp) sens = ft_getopt(varargin, 'sens', []); geomfile = ft_getopt(varargin, 'geomfile', [])

Boris Reuderink - 2012-10-10 14:15:22 +0200

Moved bugs from Christiano Michelli to joint development user.

Lilla Magyari - 2012-11-09 12:06:38 +0100

(In reply to comment #1) This is an old bug. The documentation will be updated when the recent development of the code will be ready. For the time being, I assign this for myself.

Robert Oostenveld - 2012-11-16 10:19:43 +0100

Johannes, I think you better do this. Please provide refs to some literature (not too many) and please also add those refs at

Robert Oostenveld - 2015-11-23 14:11:58 +0100

I reassign this to Simon, who will look at the existing documentation at move it over to the final destination and clean it up. Furthermore, the presence of the test script and test data need to be checked. The documentation will share sections with the EEG BEM documentation on headmodel_eeg.

Robert Oostenveld - 2015-12-16 17:28:03 +0100

(In reply to Robert Oostenveld from comment #4) reminder to Simon, please attend to this and invite the others from Muenster

Simon - 2016-01-04 10:22:46 +0100

I updated some pictures in the tutorial and checked documentation. The presented codes runs fine and the data is in the right place. The test script also exists and runs fine for me.

Robert Oostenveld - 2016-01-04 15:46:23 +0100

I have reviewed the development figure/flowchart at the start of the page. All issues have been dealt with, So I have removed it. Furthermore, I have removed the "development" warning, since the tutorial works fine.

Robert Oostenveld - 2016-01-04 15:59:32 +0100

I have moved the existing page over to Furthermore, I have given it some tags to link it automatically to other pages. I renamed the existing to and made a placeholder on the original headmodel_eeg page that links to both. I also included links to both on