[FieldTrip] extracting the transfomation matrix when using ft_volumenormalize

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

Hi Frans,

It could very well be that the organisation of the relevant data has been renamed since 2012. Typically, the philosophy is to not store downstream computation relevant stuff in an output.cfg.<> field anymore. Perhaps the information that you need is stored in output.params?

Best wishes,
Jan-Mathijs


On 18 Dec 2023, at 15:48, Frans Nord via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear fieldtrippers,

I was looking into alternatives to go from subject space to MNI space in my source reconstruction and stumbled upon this old thread https://mailman.science.ru.nl/pipermail/fieldtrip/2012-October/031673.html<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2012-October%2F031673.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C5773634ede8b4d7b547308dc06c432d9%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638392686922767431%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HH6DBuPZZLRcMuATkZNIVtkc%2BNU5mtdKaZ6A2CtBVq0%3D&reserved=0> where the following is stated:
"

-Take an individual MRI (that is coregistered to the individual's head, i.e. it has a transform that defines the head coordinate system correctly).
-Call ft_volumenormalise (with cfg.nonlinear = 'no')
-The output volume (let's call this variable normalise) contains a transformation matrix in normalise.cfg.final, that transforms from head space into 'MNI-space'.

"

When I'm trying to implement this I load a T1 and perform ft_volumerealign to co-register to acpc coordinates interactively. I then do as suggested with ft_volumenormalize with cfg.nonlinear='no' but end up without the matrix in normalise.cfg.final. Am I doing something wrong or has the functionality changed?

Best,
Frans
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https://doi.org/10.1371/journal.pcbi.1002202

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