[FieldTrip] source pos dimensions ft_sourcestatistics

[Stephen Whitmarsh]

Hi Jan-Mathijs,

Indeed, adding a .dim field did it!

Thanks again,
Stephen

On 24 June 2017 at 09:30, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Stephen,
>
> The error suggests that Fieldtrip does not manage to guess whether the set
> of dipole positions are defined on a regular grid, or whether it’s on a 2D
> mesh. Your source structure either needs a ‘dim’ field (if indeed the
> positions describe a full 3D grid in an ordered way), or it needs a ‘tri’,
> defining the edges between the nodes.
>
> Best,
> JM
>
>
> J.M.Schoffelen, MD PhD
> Senior Researcher, VIDI-fellow - PI, language in interaction
> Telephone: +31-24-3614793 <+31%2024%20361%204793>
> Physical location: room 00.028
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
> On 23 Jun 2017, at 16:28, Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
> wrote:
>
> Dear Jan-Mathijs,
>
> Thanks, I've been away but back on it now.
> I've been going over it again, and while plotting works fine (after
> sourceinterpolate), sourcestatistics still throws the same error. Just to
> be clear - i am using/creating current source-level datastructures and
> without complicating things, I end up with the following data structures
> that go into sourceanalysis.
>
>          pos: [2982×3 double]
>         freq: 10.5000
>          cfg: [1×1 struct]
>           MI: [2982×1 double]
>       inside: [2982×1 logical]
>     MIdimord: 'pos'
>
> The error I keep getting is:
>
> Error using spm_bwlabel
> spm_bwlabel: CONN must be 6, 18 or 26
>
> Error in clusterstat (line 222)
>       [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims);
>
> Error in ft_statistics_montecarlo (line 347)
>   [stat, cfg] = clusterstat(cfg, statrand, statobs);
>
> Error in ft_sourcestatistics (line 205)
>   [stat, cfg] = statmethod(cfg, dat, design);
>
> It's a mystery what might be wrong. Would you have any further leads?
>
> Thanks again,
> Stephen
>
> On 18 May 2017 at 21:35, Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Stephen,
>>
>> source2full and source2sparse are probably quite outdated, and do not
>> seem to work well anymore with the latest type of source-level data
>> structures. Most relevantly, the inside field these days is by default a
>> boolean vector of size nposx1, whereas once upon a time the inside and
>> outside fields together contained the indices of the dipole positions,
>> indicating which positions are on the in-/outside.
>>
>> Do you need the source2sparse step to begin with?
>>
>> Best,
>> JM
>>
>>
>>
>> On 17 May 2017, at 16:46, Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
>> wrote:
>>
>> Hi there,
>>
>>
>> After beamformer sourceanalysis I end up with datastructures looking like:
>>
>>   struct with fields:
>>
>>          freq: 10.5000
>>           cfg: [1×1 struct]
>>           pos: [2982×3 double]
>>           pow: [2982×1 double]
>>        inside: [2982×1 logical]
>>     powdimord: 'pos'
>>
>> The .inside field is created by ft_selectdata used to average across
>> frequencies, and contains all 1s. Running sourceanalysis with this data
>> trows the following error:
>>
>>
>> Error using spm_bwlabel
>> spm_bwlabel: CONN must be 6, 18 or 26
>>
>> Error in clusterstat (line 222)
>>       [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims);
>>
>> Error in ft_statistics_montecarlo (line 347)
>>   [stat, cfg] = clusterstat(cfg, statrand, statobs);
>>
>> Error in ft_sourcestatistics (line 205)
>>   [stat, cfg] = statmethod(cfg, dat, design);
>>
>> *222 *      [negclusobs, negnum] = spm_bwlabel(tmp, 2*numdims);
>>
>>
>> I think this results because of a wrong estimate of the dimensionality,
>> resulting from the fact that the data is represented in an array rather
>> than a 3-dimensional matrix, which it seems to expect.
>>
>> I think therefor that I might need to convert my data back into a 3-d
>> representation, i..e not a sparse but full representation. I have tried
>> using ft_source2full, but that is not straightforward as I only have inside
>> voxels/positions. In other words, I would need to do exactly the same as
>> ft_source_statistics seems to want to do with spm_bwlabel.
>>
>> So I guess I might just have put FieldTrip on the wrong leg, to use a
>> Dutch expression.
>>
>> Any suggestions?
>>
>> Best,
>> Stephen
>>
>>
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