[FieldTrip] Source locations onto an anatomical label in an atlas

[Sara Noriega Casuso]

Hi Eelke,

I have spoken with some colleagues and I think that my error arises from my
Matlab version.

Thank you for your attention!
Sara


El mar., 21 may. 2019 a las 10:25, Eelke Spaak (<e.spaak at donders.ru.nl>)
escribió:

> Hi Sara,
>
> I unfortunately still cannot reproduce your error. When I check out the
> same FT version as you're using, I get the following atlas structure:
>
> >> atlas =
> ft_read_atlas('~/repos/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii')
> Rescaling NIFTI: slope = 1, intercept = 0
>
> atlas =
>
>   struct with fields:
>
>             dim: [91 109 91]
>             hdr: [1×1 struct]
>       transform: [4×4 double]
>            unit: 'mm'
>          tissue: [91×109×91 double]
>     tissuelabel: {1×116 cell}
>        coordsys: 'mni'
>
> Could you check whether you have perhaps multiple FT versions on your
> path? The easiest is to do the following:
>
> >> restoredefaultpath(); addpath('~/repos/fieldtrip/'); ft_defaults();
>
> Of course replacing the FT path with the one appropriate for you.
>
> Let me know whether it works!
>
> Cheers,
> Eelke
>
>
>
>
> On Mon, 20 May 2019 at 09:11, Sara Noriega Casuso <
> sara.noriega at alumni.mondragon.edu> wrote:
>
>> Hi Eelke,
>>
>> Thank you for the response.
>> I have just downloaded the last version (Fieldtrip-20190419), but I still
>> have problems.
>> The error that I get is the same:
>>
>> *Reference to non-existent field 'tissue'.*
>>
>>
>> *Error in getsubfield (line 45)*
>>
>> *  s = s.(t{k});*
>>
>>
>> *Error in ft_sourceinterpolate (line 215)*
>>
>> *  if ~iscell(getsubfield(functional, cfg.parameter{i}))*
>>
>>
>> Thank you,
>>
>> Sara
>>
>>
>> El lun., 20 may. 2019 a las 8:48, Eelke Spaak (<e.spaak at donders.ru.nl>)
>> escribió:
>>
>>> Hi Sara,
>>>
>>> Are you using a recent version of FieldTrip? I think the fields
>>> atlas.brick0 etc. have long been replaced with atlas.tissue. Let me
>>> know if the issue persists if you use a recent FT.
>>>
>>> Cheers,
>>> Eelke
>>>
>>> On Sat, 18 May 2019 at 18:30, Sara Noriega Casuso
>>> <sara.noriega at alumni.mondragon.edu> wrote:
>>> >
>>> > Hello all,
>>> >
>>> > I have performed source reconstruction and now I want to interpolate
>>> an atlas onto my sourcemodel, and I am following this tutorial:
>>> >
>>> http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations/
>>> >
>>> > I have downloaded the source model: standard_sourcemodel3d10mm.mat and
>>> the atlas ROI_MNI_V4.nii mentioned in the tutorial and computed this code:
>>> >
>>> >    > atlas_MNI = ft_read_atlas('ROI_MNI_V4.nii');
>>> >
>>> >    > load('standard_sourcemodel3d10mm.mat')
>>> >
>>> >
>>> >
>>> >    >  cfg = [];
>>> >
>>> >    > cfg.interpmethod = 'nearest';
>>> >
>>> >    > cfg.parameter = 'tissue';
>>> >
>>> >    > sourcemodel2 = ft_sourceinterpolate(cfg, atlas_MNI, sourcemodel);
>>> >
>>> >
>>> > However, I get this error:
>>> >
>>> >
>>> > Reference to non-existent field 'tissue'.
>>> >
>>> >
>>> > Error in getsubfield (line 45)
>>> >
>>> >   s = s.(t{k});
>>> >
>>> >
>>> > Error in ft_sourceinterpolate (line 215)
>>> >
>>> >   if ~iscell(getsubfield(functional, cfg.parameter{i}))
>>> >
>>> >
>>> > The atlas_MNI structure is defined as:
>>> >             dim: [91 109 91]
>>> >             hdr: [1×1 struct]
>>> >       transform: [4×4 double]
>>> >            unit: 'mm'
>>> >        coordsys: 'unknown'
>>> >          brick0: [91×109×91 uint16]
>>> >     brick0label: {1×9170 cell}
>>> >
>>> > And the sourcemodel is:
>>> > dim: [18 21 18]
>>> >        pos: [6804×3 double]
>>> >     inside: [6804×1 logical]
>>> >        cfg: [1×1 struct]
>>> >       unit: 'cm'
>>> >
>>> > I know that the units are not equal, but the error does not come from
>>> that argument.
>>> > Someone knows how can I handle this error?
>>> >
>>> > Thank you in advance,
>>> > Sara
>>> >
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > fieldtrip mailing list
>>> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> > https://doi.org/10.1371/journal.pcbi.1002202
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
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