[FieldTrip] Source localization

Hanneke van Dijk Hanneke.vanDijk at med.uni-duesseldorf.de
Wed Jan 23 12:19:37 CET 2013 

Hi Casper,

The cfg.anaparameter should then be 'anatomy'.  It refers to the field (in
data) in which the anatomy can be found, in your case: data.anatomy.

Hope this helps,

Hanneke
Op 23 jan. 2013 10:57 schreef "Casper van Heck" <caspervanheck at gmail.com>
het volgende:

> Dear Jan-Mathijs,
>
> Since ft_sourceplot complained about not having anatomy (or functional)
> parameter, and it seems to default to a field named '*data.anatomy'*, I
> assumed adding *mri.anatomy* in *data.anatomy* would suffice.
>
> But, without this, ft_sourceplot would again require an anatomy parameter,
> so that would mean that I need to ut '*cfg.anaparameter = mri*' in the
> cfg I feed to ft_sourceplot, where 'mri' is the result from
> ft_volumereslice.
> However, ft_sourceplot then says "*do not understand cfg.anaparameter*",
> and thus it is not plotting "*anatomy*". After looking back to the
> plotting tutorial where I read "The anatomy can be read with ft_read_mri",
> I'm not quite sure what's going wrong.
>
> Sincerely,
>
> Casper
>
>
>
> On Tue, Jan 22, 2013 at 9:49 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi intersect(everyone, casper)
>>
>> Everyone,
>>
>> While the whole script is way too convoluted to put up here, but luckily
>> the relevant steps are quite simple
>> Input is simply raw data, read with ft_preprocessing, which is passed
>> through functions as shown in my previous email.
>>
>> After passing the data to ft_sourcegrandaverage (only using
>> cfg.outputfile), where the data is fed as a cell array (which seems to work
>> properly), I go over to a source-comparison script. This script works as
>> follows:
>> First I create a pre-post contrast as shown in the beamformer tutorial.
>>
>> Next, I read some MRI-data using ft_read_mri from a standard folder, and
>> reslice this data:
>> *mri = ft_read_mri(strcat(h.subject,'Subject01.mri'));
>> *
>> *mri = ft_volumereslice([], mri);*
>>
>> Then:
>> *[data] = ft_sourceinterpolate(cfg, data, mri);
>> *
>> where cfg contains:
>> *cfg.parameter: 'avg.pow'*
>> *cfg.downsample: 4*
>>
>> and I add the anatomy:
>> *data.anatomy = mri.anatomy; clear mri*
>>
>>
>> Putting mri.anatomy into data.anatomy is probably not what you want to
>> do: the whole point about ft_sourceinterpolate is to get the functional and
>> anatomical data in the same 'pixel-space'; this is the only way that
>> ft_sourceplot (as of yet) can deal with it. The reason is that now the
>> functional data is sampled once every 4 voxels, relative to the anatomy. I
>> guess that this causes your problem in ft_sourceplot.
>>
>>
>>
>> Best wishes,
>>
>> Jan-Mathijs
>>
>>
>>
>> And finally, I call ft_sourceplot using these options:
>>
>> cfg.*parameter: 'avg.pow';*
>>
>> *cfg.downsample: 4*
>>
>> *
>> *
>>
>> with one of these three methods:
>> 1) *cfg.method = 'surface';*
>> *    cfg.surffile = 'surface_l4_both.mat';*
>> *    cfg.surfdownsample = 4;*
>> *    cfg.projmethod = 'nearest';*
>> 2) *cfg.method = 'ortho';*
>> 3) *cfg.method = 'slice';*
>> *    cfg.nslices = 20;*
>> Which leads to the errors shown earlier. At this point, disp(data) yields:
>> *K>> disp(data)*
>> *         avg: [1x1 struct]*
>> *         pos: [16777216x3 double]*
>> *         dim: [256 256 256]*
>> *      inside: [1x16777216 double]*
>> *     outside: [1x0 double]*
>> *    coordsys: 'ctf'*
>> *        unit: 'mm'*
>> *         cfg: [1x1 struct]*
>> *     anatomy: [256x256x256 double]*
>> *
>> *
>> I'm guessing it has something to do with the 'inside' and 'outside'
>> elements, so my 'standard head model'. I think I made this using the
>> following code:
>> *mri = ft_read_mri(strcat(h.subject,'Subject01.mri')); % load 'standard'
>> anatomical model
>> *
>> *
>> *
>> *% segment the template brain and construct a volume conduction model
>> (i.e. head model)*
>> *cfg             = [];*
>> *cfg.output      = {'brain' 'scalp' 'skull'};*
>> *cfg.downsample  = 2;*
>> *t_seg    = ft_volumesegment(cfg, mri);*
>> * *
>> *% create head model*
>> *cfg          = [];*
>> *cfg.method   = 'singlesphere';*
>> *cfg.hdmfile  = strcat(h.subject,'Subject01.hdm');*
>> *cfg.elec     = ft_read_sens('standard_1020.elc');*
>> *t_vol = ft_prepare_headmodel(cfg, t_seg);*
>> *clear template_seg*
>> *
>> *
>> *% construct the dipole grid in the template brain coordinates*
>> *cfg = [];*
>> *cfg.normalize = 'no'; % no normalization, since we're comparing two
>> conditions THAT'S RIGHT I DID PAY ATTENTION*
>> *cfg.vol        = t_vol;*
>> *t_grid  = ft_prepare_sourcemodel(cfg);*
>> *
>> *
>> After which I use this on all subjects, using this (note that I store all
>> data in a single massive structure, to make saving to disk and selecting
>> data etc. easier):
>> *source{subj}.(datasets{d}) = sourceanalysis(data, t_vol, t_grid);*
>> *
>> *
>> Anyone seeing anything obviously stupid?
>>
>> Sincerely,
>>
>> Casper
>>
>>
>> On Fri, Jan 18, 2013 at 4:43 PM, <Lilla.Magyari at mpi.nl> wrote:
>>
>>> Hi Casper,
>>>
>>> I think it is really difficult to figure only from the error message what
>>> the problem is. I think it would be also useful to see the inputs (cfg,
>>> and your data) of ft_sourceplot. Could you just send me how your cfg and
>>> your data-structure looks like? (I mean that you do not need to send the
>>> actual data, just the screen output of disp(data) and disp(cfg)).
>>>
>>> Best,
>>> Lilla
>>>
>>>
>>> > Dear Fieldtrippers,
>>> >
>>> > I've asked this question earlier, but either it got lost due to
>>> technical
>>> > reasons, or the people who actually understand what's happening here
>>> were
>>> > on vacation, so here it is again:
>>> >
>>> > I've been trying to do a source analysis on a dataset with two
>>> conditions,
>>> > mostly following the tutorials and examples from the Fieldtrip site,
>>> and
>>> > come upon a problem; it won't plot. While the source analysis is not an
>>> > essential component of the analysis of this dataset (it's more along
>>> the
>>> > lines of "let's see if I can do this"), and I don't expect any result
>>> > other
>>> > than something like "there might be a source in the left hemisphere",
>>> I'd
>>> > still would like to found out why it's not working.
>>> >
>>> > Essentially, I create a standard headmodel cause I don't have
>>> individual
>>> > MRI's from the "Subject1.mri"-example, using ft_volumesegment,
>>> > ft_prepare_headmodel and ft_prepare_sourcemodel, and try to get
>>> Fieldtrip
>>> > to find sources based on individual EEG-datasets using ft_freqanalysis
>>> > (with cfg.method = 'mtmfft') and ft_sourceanalysis.
>>> > After that, I use ft_sourcegrandaverage to produce, well, a grand
>>> average
>>> > source, and feed this via ft_sourceinterpolate to ft_sourceplot.
>>> >
>>> > Now, ft_sourceplot has three plotting possibilities: slice, ortho, and
>>> > surface. Initially I tried to get the ortho-option to work, but this
>>> gave
>>> > the following error:
>>> > *Attempted to access dim(3); index out of bounds because numel(dim)=2.*
>>> > *Error in ==> cornerpoints at 11
>>> > *
>>> > *Error in ==> ft_plot_slice at 157
>>> > *
>>> >
>>> > So, I tried the surf-option, which gave me this:
>>> > *Undefined function or variable "val".*
>>> > *Error in ==> ft_sourceplot at 1174
>>> > *
>>> >
>>> > And finally, I tried the slice-option, which gave one of two errors
>>> (which
>>> > seems to be based on how many slices I requested):
>>> > *Out of memory*
>>> > Which is pretty damn impressive since I've got 8GB of RAM and a
>>> pagefile
>>> > topping of at 40GB
>>> > Or, the mildly disconcerting:
>>> > *Matlab has encountered an internal error and has to close*
>>> > Which seems to have been caused by a so-called *"Segmentation
>>> violation"
>>> > *
>>> >
>>> > Can anyone offer any insight in these errors? I think I'm doing
>>> something
>>> > wrong pretty early on, but have no idea what it is.
>>> >
>>> > Sincerely,
>>> >
>>> > Casper van Heck
>>> >
>>> >
>>> > On Fri, Dec 21, 2012 at 1:43 PM, Casper van Heck
>>> > <caspervanheck at gmail.com>wrote:
>>> >
>>> >> Dear Fieldtrippers,
>>> >>
>>> >> I've been trying to do a source analysis on a dataset with two
>>> >> conditions,
>>> >> mostly following the tutorials and examples from the Fieldtrip site,
>>> and
>>> >> come upon a problem; it won't plot. While the source analysis is not
>>> an
>>> >> essential component of the analysis of this dataset (it's more along
>>> the
>>> >> lines of "let's see if I can do this"), and I don't expect any result
>>> >> other
>>> >> than something like "there might be a source in the left hemisphere",
>>> >> I'd
>>> >> still would like to found out why it's not working.
>>> >>
>>> >> Essentially, I create a standard headmodel cause I don't have
>>> individual
>>> >> MRI's from the "Subject1.mri"-example, using ft_volumesegment,
>>> >> ft_prepare_headmodel and ft_prepare_sourcemodel, and try to get
>>> >> Fieldtrip
>>> >> to find sources based on individual EEG-datasets using ft_freqanalysis
>>> >> (with cfg.method = 'mtmfft') and ft_sourceanalysis.
>>> >> After that, I use ft_sourcegrandaverage to produce, well, a grand
>>> >> average
>>> >> source, and feed this via ft_sourceinterpolate to ft_sourceplot.
>>> >>
>>> >> Now, ft_sourceplot has three plotting possibilities: slice, ortho, and
>>> >> surface. Initially I tried to get the ortho-option to work, but this
>>> >> gave
>>> >> the following error:
>>> >> *Attempted to access dim(3); index out of bounds because
>>> numel(dim)=2.*
>>> >> *Error in ==> cornerpoints at 11
>>> >> *
>>> >> *Error in ==> ft_plot_slice at 157
>>> >> *
>>> >>
>>> >> So, I tried the surf-option, which gave me this:
>>> >> *Undefined function or variable "val".*
>>> >> *Error in ==> ft_sourceplot at 1174
>>> >> *
>>> >>
>>> >> And finally, I tried the slice-option, which gave one of two errors
>>> >> (which
>>> >> seems to be based on how many slices I requested):
>>> >> *Out of memory*
>>> >> Which is pretty damn impressive since I've got 8GB of RAM and a
>>> pagefile
>>> >> topping of at 40GB
>>> >> Or, the mildly disconcerting:
>>> >> *Matlab has encountered an internal error and has to close*
>>> >> Which seems to have been caused by a so-called *"Segmentation
>>> violation"
>>> >> *
>>> >>
>>> >> Can anyone offer any insight in these errors? I think I'm doing
>>> >> something
>>> >> wrong pretty early on, but have no idea what it is.
>>> >>
>>> >> Sincerely,
>>> >>
>>> >> Casper van Heck
>>> >>
>>> > _______________________________________________
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>>> > fieldtrip at donders.ru.nl
>>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
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>>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>    Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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