[FieldTrip] a problem with creating a ROI mask

Shen-Mou Hsu explena at gmail.com
Wed Mar 31 12:33:15 CEST 2021


Dear Jan-mathijs,

1. Many thanks for your insights. Adding "sourcemodel.coordsys = ‘mni’"
does work now!

2. No problem! We will look into the code to see if there is something that
we may contribute.

Best,
Shen-Mou

On Tue, Mar 30, 2021 at 6:34 PM Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Shen-Mou,
>
> I think that you need to ensure that:
>
> -the metrical units in both atlas and sourcemodel are the same, consider
> calling ft_convert_units(sourcemodel, ‘mm’); before proceeding.
> -the coordinate systems of both objects are the same.
>
> I see that, upon loading the atlas, that the coordsys field is ‘mni’.
> Sourcemodel does not have a coordsys field, which explains why you need to
> change the anatomical labels (from unknown to something more meaningful). I
> expect that ‘mni’ is not a coordsys that is outputted after this step (most
> likely it will be ‘acpc’). This is subsequently detected as a mismatch, and
> may have contributed to the error you got.
>
> What happens if you explicitly state sourcemodel.coordsys = ‘mni’ (in
> addition to the metric units conversion)?
>
> Note, ft_volumelookup is a very ‘old’ function (and rarely used by people
> that are close to the core developers), thus it might not have grown along
> with the rest of the codebase in terms of data bookkeeping and overall code
> consistency. If you see room for improvement, we look forward to suggested
> code changes as Pull Requests in the FieldTrip github repository!
>
> Best wishes,
> Jan-mathijs
>
>
>
> On 29 Mar 2021, at 12:14, Shen-Mou Hsu <explena at gmail.com> wrote:
>
> Dear FieldTrip community,
>
> I try to follow this instruction (
> https://www.fieldtriptoolbox.org/tutorial/salzburg/#perform-sourcanalysis)
> to create a ROI mask as follows:
>
> atlas = ft_read_atlas(fullfile(ftpath,
> 'template/atlas/aal/ROI_MNI_V4.nii'));
> sourcemodel = load(fullfile(ftpath,
> 'template/sourcemodel/standard_sourcemodel3d10mm'));
>
> cfg = [];
> cfg.atlas = atlas;
> cfg.roi = atlas.tissuelabel(43);
> mask = ft_volumelookup(cfg, sourcemodel);
>
> However, after executing these lines, an instruction popped out and asked
> "Do you want to change the anatomical labels for the axes [Y, n]?". After
> specifying  the MNI system, there was still an error message "Error using
> ft_volumelookup (line 248) the mismatch between the coordinate system in
> the atlas and the coordinate system in the data cannot be resolved"
>
> Any help will be much appreciated!
> Shen-Mou Hsu
>
>
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