[FieldTrip] fs_LR mesh in MNI-space

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

Ciao Roberto and Paolo,

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): https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02673.html. 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.

Best wishes, and happy reading,

JM





On 24 Aug 2020, at 16:20, Paolo Belardinelli <paolo.belardinelli at gmail.com<mailto:paolo.belardinelli at gmail.com>> wrote:

Hi Robert.

I came with the same question at the end of last year.

Jan Mathijs gave me the following answer:

"I don’t know what the exact motivation would be for you to get the
MNI coordinates, but if you want to do this in a rigorous and correct
way, you probably want to check out the original post freesurfer
processing script that is used in the structural processing pipeline
of the HCP. I used a(n older) version of the code that can be found
here: https://github.com/Washington-University/HCPpipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

Alternatively, if you are looking for an approximation, you could
estimate the normalisation parameters from a call to
ft_volumenormalise, with the subject’s anatomical MRI in the input
(ensuring it to be in the same coordinate space as your meshes, and
both probably in ‘mm’ (ft_convert_units) ), and use ft_warp_apply on
the mesh.pos to get the ‘MNI coordinates’."

At the time I went for the approximate solution but I have still to
implement the rigorous way.

Best wishes,

Paolo


On Mon, Aug 24, 2020 at 4:08 PM Robert Seymour
<robert.seymour at students.mq.edu.au<mailto:robert.seymour at students.mq.edu.au>> wrote:

Hi all,

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.

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.

Thanks,

Rob Seymour




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--
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478

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