Re: [HCP-Users] ft_read_cifti too many grayordinates

[Harms, Michael]

Hi, No such option in ft_read_cifti currently. I've added Robert in case he wants to comment. You should be able to remove the NaN and get a standard ordering.  If you want to check, you can use the 'ciftiopen.m' alternative for loading CIFTI and compare that you get the same ordering. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: Matthew George Liptrot <matthew.lipt...@di.ku.dk> Date: Monday, August 31, 2015 6:51 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] ft_read_cifti too many grayordinates 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" <st...@fmrib.ox.ac.uk> 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 <glass...@wusm.wustl.edu> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Janine Bijsterbosch <janine.bijsterbo...@ndcn.ox.ac.uk> Date: Monday, July 20, 2015 at 9:52 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> 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 janine.bijsterbo...@ndcn.ox.ac.uk --  Matthew George Liptrot 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users