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

[Eelke Spaak]

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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