[FieldTrip] ft_sourceinterpolate question

[Bear, Joshua]

Hi Robert,

Thank you so much for the response!

My ultimate intention is actually to use the parcellation scheme proposed by Gordon et al. (Cerebral Cortex, Volume 26, Issue 1, 1 January 2016, Pages 288–303, https://doi.org/10.1093/cercor/bhu239) though at this time I was using the atlas provided in the tutorial.

The problem I ran into is that I am trying to interpolate my brain’s mesh DOWN from 15002 to 8004 (to match the atlas), not up. As you pointed out, I have had some problems with other high resolution meshes, but in this case ft_sourceinterpolate seemed to work — it just only worked for one of the two dimensions of my connectivity data. That is, it went from a [15002×15002 double] to a [8004×15002 double]. Of course it’s possible the interpolation for that first dimension was incorrect, but what confused me was that it did not interpolate the second dimension. (As I write this, I’m wondering if I should simply try transposing the matrix and running the interpolation again!).

I will try, as you suggest, downsampling the mesh externally and trying again. I’m not able to match the 8004 vertices perfectly, but perhaps if I drop it slightly below this number it will be able to interpolate up correctly.

Any other thoughts or suggestions are greatly appreciated as well.

Best,
Josh



From: <fieldtrip-bounces at science.ru.nl> on behalf of "Seymour, Robert (Research Student)" <seymourr at aston.ac.uk>
Reply-To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Date: Wednesday, April 25, 2018 at 5:48 PM
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] ft_sourceinterpolate question

Hi Josh,

It seems like you are using the HCP Glasser atlas ('A multi-modal parcellation of human cerebral cortex')? The atlas presented as part of the network analysis tutorial is designed for a cortical mesh with 8004 vertices, rather than the 15002 you are using. I don’t believe ft_sourceinterpolate can currently cope with the surface-based transformation upwards from 8000—> 15000 vertices.

To use the HCP atlas you will need to downsample the original 32k atlas in fs_LR space to 15000 space and transform to whichever standard-brain template you are using. This is non-trivial and requires some functions from the HCP project (e.g. wb_command which can be found here: https://www.humanconnectome.org/software/workbench-command).

If your mesh is created using Freesurfer you can use this script here:

https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh

If the mesh is not constructed using Freesurfer it will be tricker & I would recommend contacting the HCP mailing list.

Good luck!

Robert Seymour (Aston Brain Centre & Department of Cognitive Science, Macquarie University).


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