It¹s best to keep CCing the list. You should indeed be able to carry out such a study. It would be easier once the diffusion data are processed a little further along (e.g. Fiber orientation modeling). As for your other e-mail and NODDI, I don¹t know what the acquisition requirements for NODDI are, but the HCP data should work for most applications.
Peace, Matt. On 2/1/16, 11:02 PM, "Georg Kerbler" <[email protected]> wrote: >Hi Matt, > >I realize the way I formulated my email sounds confusing. My main aim is >to perform tractography between a set of ROIs comprising the network that >is activated during certain functional tasks (and conditions within that >task) and then look at connectivity measures within this network and see >whether structural connectivity measures explain variability in the task >performance of subjects and possibly the amount of activation in grey >matter areas. Connectivity measures would then include FA/MD/ etc. along >white matter tracks connecting gray matter areas as you were mentioning. >Is there possibly a framework within the current HCP pipelines/commands >to achieve this? > >cheers, >Georg > >On Feb 1, 2016, at 10:00 PM, Glasser, Matthew wrote: > >> Indeed this is somewhat confusing: the task fMRI beta maps (actually it >>is Z maps that are currently mostly prominently released and any beta >>maps currently available have an issue with the bias field) are grey >>matter measures but FA/MD/AD are generally white matter measures. There >>are T1w/T2w grey matter myelin maps that are already in CIFTI space, >>perhaps this is what you are after? Alternatively, if you wanted the >>FA/MD/AD along white matter tracts that connect two greymatter regions >>that might make sense too (this could be done by computing the >>tractography from the cortical surface and to the cortical surface >>through the white matter, thresholding the tract to make a volume mask, >>and computing the mean white matter measures inside the mask. >> >> Peace, >> >> Matt. >> >> From: <[email protected]> on behalf of Timothy >>Coalson <[email protected]> >> Date: Monday, February 1, 2016 at 12:46 AM >> To: Stephen Smith <[email protected]> >> Cc: "[email protected]" <[email protected]> >> Subject: Re: [HCP-Users] Converting FA maps to CIFTI >> >> That was meant to say "take the part of your measures that is in grey >>matter". >> Tim >> On Feb 1, 2016 7:45 AM, "Timothy Coalson" <[email protected]> wrote: >>> So, you can make cifti files that contain white matter, but they won't >>>match up to our grey matter cifti files. If you want to take the past >>>of your measures that is in grey matter and put that into cifti, you >>>first need to use -volume-to-surface-mapping for both hemispheres, then >>>you can use -cifti-create-dense-from-template or similar. >>> Tim >>> On Feb 1, 2016 7:20 AM, "Stephen Smith" <[email protected]> wrote: >>>> Hi - so you have estimated in FA, MD, etc in grey matter? >>>> Note that CIFTI doesn't cover white matter. >>>> Cheers. >>>> >>>> >>>> >>>>> On 1 Feb 2016, at 06:01, Georg Kerbler <[email protected]> wrote: >>>>> >>>>> Hi, >>>>> >>>>> I would like to convert FA/MD/AD/etc. images which I calculated in >>>>>T1w space, into CIFTI's, in order to correlate/overlay them with e.g. >>>>>beta-maps from functional tasks. >>>>> >>>>> What is the best way to do this? >>>>> >>>>> Thanks for your help, >>>>> Best, >>>>> Georg >>>>> >>>>> P.s.: So far I used 'wb_command -cifti-convert -from-nifti <nifti >>>>>in> <template cifti> <cifti out>'; however opening the resulting >>>>>image in wb_view doesn't display anything. >>>>> (Prior to using the command I transformed the DTI images into >>>>>MNInonlinear space - by registering them to the T1 in the >>>>>MNInonlinear folder and then warping the images) >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>>> >>>> >>>>----------------------------------------------------------------------- >>>>---- >>>> Stephen M. Smith, Professor of Biomedical Engineering >>>> Head of Analysis, Oxford University FMRIB Centre >>>> >>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>> +44 (0) 1865 222726 (fax 222717) >>>> [email protected] http://www.fmrib.ox.ac.uk/~steve >>>> >>>>----------------------------------------------------------------------- >>>>---- >>>> >>>> Stop the cultural destruction of Tibet >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> HCP-Users mailing list >>>> [email protected] >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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. 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