[FieldTrip] source pos dimensions ft_sourcestatistics
Stephen Whitmarsh
stephen.whitmarsh at gmail.com
Mon Jun 26 13:42:58 CEST 2017
Hi again Mathijs :-)
The problem seems to be shifted toward the next step: I now want to
visualize the stats on an anatomical image (the same template on which the
subject inverse headmodels were based). For this I need to interpolate, but
that breals. The following datasets go into ft_sourceinterpolate:
stat =
struct with fields:
prob: [2982×1 double]
posclusters: [1×3 struct]
posclusterslabelmat: [2982×1 double]
posdistribution: [1×1000 double]
negclusters: [1×4 struct]
negclusterslabelmat: [2982×1 double]
negdistribution: [1×1000 double]
cirange: [2982×1 double]
mask: [2982×1 logical]
stat: [2982×1 double]
ref: [2982×1 double]
dimord: 'pos'
dim: [17 20 17]
freq: 10.5000
pos: [2982×3 double]
cfg: [1×1 struct]
and:
template_mri =
struct with fields:
dim: [91 109 91]
anatomy: [91×109×91 double]
hdr: [1×1 struct]
transform: [4×4 double]
unit: 'mm'
coordsys: 'spm'
inside: [91×109×91 logical]
Now, if I run the following:
cfg = [];
cfg.parameter = 'stat';
stat_int = ft_sourceinterpolate(cfg, stat, template_mri);
I get the following error:
Warning: could not reshape stat to the expected dimensions
> In ft_datatype_volume (line 136)
In ft_checkdata (line 351)
In ft_sourceinterpolate (line 170)
selecting subvolume of 0.0%
reslicing and interpolating stat
interpolating
Error using interpn (line 153)
Wrong number of input arguments.
Error in ft_sourceinterpolate>my_interpn (line 693)
av(sel) = interpn(fv, ax(sel), ay(sel), az(sel), interpmethod);
Error in ft_sourceinterpolate (line 595)
av( sel) = my_interpn(fv, ax(sel), ay(sel), az(sel),
cfg.interpmethod, cfg.feedback);
153 error(message('MATLAB:interpn:nargin'));
Now, I did try to add a .statdimord field, but that didn't make a
difference.
Any idea?
Thanks,
Stephen
On 26 June 2017 at 13:09, Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
wrote:
> 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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>>> fieldtrip at donders.ru.nl
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>>>
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>>
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