[FieldTrip] Problem with tutorial related to parceled brain space

[Schoffelen, J.M. (Jan Mathijs)]

Hi Xavier,

If the data object that fieldtrip uses for sourceplotting does not contain interpretable (for fieldtrip) information about the left/right orientation, fieldtrip will plot the data ‘as is’. If the volume is flipped in the box (e.g. left-handed voxel coordinate system) the left side of the head ends up on the right side of the screen, and vice versa.

Does the data object that you want to plot have a ‘coordsys’ field? If not, do you know what the interpetation of the coordinate axis are? Either way, you could use ft_determine_coordsys to check and change this. I expect that when you call ft_sourceplot on the output of this ft_determine_coordsys, the image will be displayed in neurological convention.

Good luck,
Jan-Mathijs



On 4 Dec 2023, at 15:10, Xavier Job via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hi all,

I've noticed something strange in the tutorial "Analysis of auditory evoked fields in sensor and source space" (https://www.fieldtriptoolbox.org/tutorial/salzburg/#plot-the-result-in-parceled-brain-space<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fsalzburg%2F%23plot-the-result-in-parceled-brain-space&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C50aec65b27894f964d2c08dbf63529e9%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638374480404570505%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XVPdOlvH8%2B2DHCOyycmT4FAsLUwHsMI8GGAapnFwAIc%3D&reserved=0>).

In the section "Localizing auditory evoked fields using beamforming techniques in parceled brain space", when plotting the source in parceled brain space, the left/right axis appears to be wrong. The atlas says 'Heschl L', but on the plot it's the right hemisphere. When interactively clicking on different areas, all right hemisphere areas appear as left hemisphere labels and vice versa.

I'm also trying to do this analysis on my own data and I get the same problem. When I plot the beamformer source activity evoked from a tactile stimulus delivered to the left hand, I get (largely) right SI which makes sense, but when plotting in parceled brain space this flips to the other (left) hemisphere, which is definitely wrong.

Perhaps there is a problem with which template file is used for interpolation in the tutorial? For parceled brain space, the source is first interpolated using the spm8 template (~fieldtrip/external/spm8/templates/T1.nii), but prior to that it was interpolated using another template brain (~fieldtrip/template/anatomy/single_subj_T1.nii) for plotting in 'unparceled' space.

Any help with this would be greatly appreciated!

Best,
Xavier

<Screenshot 2023-12-01 at 17.15.46.png>

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C01%7Cfieldtrip%40science.ru.nl%7C50aec65b27894f964d2c08dbf63529e9%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638374480404570505%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XU6ZzStG12f7j3HnsGGH92W7myu%2BdKkXdDO43qL%2F5SM%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20231206/c2f7a967/attachment.htm>