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Ciao Roberto and Paolo,
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<div class="">If you’re up for it: this question occurs now and then on the HCP mailing list, which, unlike me, really has some people subscribed that know what they are talking about. Perhaps if you start off with this thread, you at least get an impression
of the hairy details (I don’t know whether they managed to get to a solution): <a href="https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02673.html" class="">https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02673.html</a>. Note that
this is already a ~4 yr old thread, and it could be that there have been recent developments in software, or new insights (in other threads of said mailing list) that provide a solution.</div>
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<div class="">Best wishes, and happy reading,</div>
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<div class="">JM</div>
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<div class="">On 24 Aug 2020, at 16:20, Paolo Belardinelli <<a href="mailto:paolo.belardinelli@gmail.com" class="">paolo.belardinelli@gmail.com</a>> wrote:</div>
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<div class="">Hi Robert.<br class="">
<br class="">
I came with the same question at the end of last year.<br class="">
<br class="">
Jan Mathijs gave me the following answer:<br class="">
<br class="">
"I don’t know what the exact motivation would be for you to get the<br class="">
MNI coordinates, but if you want to do this in a rigorous and correct<br class="">
way, you probably want to check out the original post freesurfer<br class="">
processing script that is used in the structural processing pipeline<br class="">
of the HCP. I used a(n older) version of the code that can be found<br class="">
here: <a href="https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh" class="">
https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh</a><br class="">
<br class="">
Alternatively, if you are looking for an approximation, you could<br class="">
estimate the normalisation parameters from a call to<br class="">
ft_volumenormalise, with the subject’s anatomical MRI in the input<br class="">
(ensuring it to be in the same coordinate space as your meshes, and<br class="">
both probably in ‘mm’ (ft_convert_units) ), and use ft_warp_apply on<br class="">
the mesh.pos to get the ‘MNI coordinates’."<br class="">
<br class="">
At the time I went for the approximate solution but I have still to<br class="">
implement the rigorous way.<br class="">
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Best wishes,<br class="">
<br class="">
Paolo<br class="">
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On Mon, Aug 24, 2020 at 4:08 PM Robert Seymour<br class="">
<<a href="mailto:robert.seymour@students.mq.edu.au" class="">robert.seymour@students.mq.edu.au</a>> wrote:<br class="">
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Hi all,<br class="">
<br class="">
I have created both a 4k and 8k 'sourcemodel' mesh using the excellent ft_postfreesurferscript.sh script. These are registered to the fs_LR brain.<br class="">
<br class="">
I was wondering if anyone could advise the best way to register these meshes to MNI-space (i.e. to the canonical SPM brain)? My thinking is that after source analysis it would good to project the data back into volumetric space for plotting and comparing with
the previous literature etc.<br class="">
<br class="">
Thanks,<br class="">
<br class="">
Rob Seymour<br class="">
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_______________________________________________<br class="">
fieldtrip mailing list<br class="">
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https://doi.org/10.1371/journal.pcbi.1002202<br class="">
</blockquote>
<br class="">
<br class="">
<br class="">
--<br class="">
--<br class="">
Paolo Belardinelli, PhD<br class="">
Neurology Department<br class="">
University Hospital Tuebingen<br class="">
Eberhard Karls University Tuebingen<br class="">
Hoppe-Seyler Str. 3<br class="">
D-72076 Tuebingen<br class="">
Tel: +49 7071 / 29 80478<br class="">
<br class="">
_______________________________________________<br class="">
fieldtrip mailing list<br class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="">
https://doi.org/10.1371/journal.pcbi.1002202<br class="">
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