Hiya, Is there such an option with ft_read_cifti to omit these "non-standard” grayordinates?
If not, and instead we use Matlab to remove the NaN rows/columns and ‘squeeze’ the connectivity matrix, can anyone confirm that we will always get a “standard”, correctly ordered, dense connectivity matrix that we can directly compare across subjects? (I’m assuming that I always get a 96854^2 matrix from ft_read_cifti and then find and remove 5572 rows/columns of NaNs). No other gotchas, pitfalls etc? Cheers, M@ On 21/7/15 10:33 , "Stephen Smith" <[email protected]<mailto:[email protected]>> wrote: HI Matt - thanks - so is there an option with ft_read_cifti for excluding those grayordinates that are not part of the "standard" 91k set, upon read-in? Cheers On 20 Jul 2015, at 17:06, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: Some of us don’t think that code should do that. You can manually remove the NaNs, or use alternative software (option B): https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Janine Bijsterbosch <[email protected]<mailto:[email protected]>> Date: Monday, July 20, 2015 at 9:52 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] ft_read_cifti too many grayordinates Hi, When I use ft_read_cifti to load the dense connectome I end up with 96854*96854 grayordinates and lots of NaN's. This appears to be because the centre of the brain is included in the cortical surfaces, which I can remove manually to end up with the expected 91282 grayordinates and no NaN's. However, I was just wondering if this behaviour is expected and fixing it manually is ok, or if this is indicative of other associated bugs please? Thanks!! Best wishes, Janine ----- Dr Janine Bijsterbosch Postdoctoral Researcher FMRIB Centre, University of Oxford John Radcliffe Hospital Oxford, United Kingdom [email protected]<mailto:[email protected]> -- Matthew George Liptrot <http://about.me/matthewliptrot> Department of Computer Science University of Copenhagen & Section for Cognitive Systems Department of Applied Mathematics and Computer Science Technical University of Denmark http://about.me/matthewliptrot <http://about.me/matthewliptrot> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
