[FieldTrip] tissue labels in mesh for prepare head model

[Simon Homolle]

Dear John,

Can you still recall the previous and current version of fieldtrip you are using? 

I tried ft_prepare_headmodel (cfg.method =simbio) myself with the fieldtrip version from today and did not encounter this warning.
The structure of my mesh looks quite similar:

            hex: [4992121x8 double]
         labels: [4992121x1 double]
         tissue: [4992121x1 double]
    tissuelabel: {'csf'  'gray'  'scalp'  'skull'  'white'}
           unit: 'mm'
            cfg: [1x1 struct]
            pos: [5105088x3 double]
         inside: [5105088x1 logical]

Simon Homölle
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Phone: +31-(0)24-36-65059

> On 11 Jul 2016, at 04:14, RICHARDS, JOHN <RICHARDS at mailbox.sc.edu> wrote:
> 
> I switched a couple of months ago to a version of FT.  I am using simbio meshes and ft_prepare_headmodel for a FEM source analysis.
> 
> This is the code to prepare the mesh:  (mri.tissuelabel is in the mri structure).
> cfg        = [];
> cfg.shift  = 0.3;
> cfg.method = 'hexahedral';
> cfg.tissue = mri.tissuelabel;
> mesh = ft_prepare_mesh(cfg,mri);
> 
> This results in a struct with
> hex
> labels
> tissue
> tissuelabel
> 
> When I run 
> cfg        = [];
> cfg.method ='simbio';
> cfg.conductivity=conductivity1;
> vol        = ft_prepare_headmodel(cfg, mesh);    
> 
> I get several instances warnings (see below).  The warnings are because the getdimord does not recognize “labels” and “tissue”.  But the ft_headmodel_simbio needs the tissue to tell which tissues to assign conductivity to a hex voxel.  See header of the ft_headmodel_simbio, designates hex, tissue, and tissuelabel.  
> 
> This used to work in the previous version; it may still be working just giving a warning.
> 
> Any help?
> 
> John
> 
> E.g., from header
> Use as
>    headmodel = ft_headmodel_simbio(mesh,'conductivity', conductivities, ...)
> 
>  The mesh is given as a volumetric mesh, using ft_datatype_parcellation
>    mesh.pos = vertex positions
>    mesh.tet/mesh.hex = list of volume elements
>    mesh.tissue = tissue assignment for elements
>    mesh.tissuelabel = labels correspondig to tissues
> 
>  Required input arguments should be specified in key-value pairs and have
> 
> Warning: could not determine dimord of "tissue" in the following data 
>> In getdimord (line 549)
>  In ft_datatype_source (line 232)
>  In ft_datatype_parcellation (line 178)
>  In ft_headmodel_simbio (line 46)
>  In ft_prepare_headmodel (line 430)
>  In CreateFieldtripHeadModels (line 348) 
>            hex: [1440558x8 double]
>         labels: [1440558x1 double]
>         tissue: [1440558x1 double]
>    tissuelabel: {'wm'  'gm'  't2wcsf'  'dura'  'skull'  'scalp'  'head'  'eyes'  'nasalcavity'  'nma_pve'}
>           unit: 'mm'
>            cfg: [1x1 struct]
>            pos: [1487661x3 double]
>         inside: [1487661x1 logical]
> 
> AND
> 
> Warning: could not determine dimord of "labels" in the following data 
>> In getdimord (line 549)
>  In ft_datatype_source (line 232)
>  In ft_datatype_parcellation (line 178)
>  In ft_headmodel_simbio (line 46)
>  In ft_prepare_headmodel (line 430)
>  In CreateFieldtripHeadModels (line 348) 
>            hex: [1440558x8 double]
>         labels: [1440558x1 double]
>         tissue: [1440558x1 double]
>    tissuelabel: {'wm'  'gm'  't2wcsf'  'dura'  'skull'  'scalp'  'head'  'eyes'  'nasalcavity'  'nma_pve'}
>           unit: 'mm'
>            cfg: [1x1 struct]
>            pos: [1487661x3 double]
>         inside: [1487661x1 logical]
> 
> ***********************************************
> John E. Richards Carolina Distinguished Professor
> Department of Psychology
> University of South Carolina
> Columbia, SC  29208
> Dept Phone: 803 777 2079
> Fax: 803 777 9558
> HTTP: jerlab.psych.sc.edu
> ***********************************************
> 
> 
> 
> 
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