[FieldTrip] Source localization

Casper van Heck caspervanheck at gmail.com
Wed Jan 23 10:55:54 CET 2013 

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
>> >>
>> > _______________________________________________
>> > fieldtrip mailing list
>> > fieldtrip at donders.ru.nl
>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
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>>
>
> _______________________________________________
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> 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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