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]<mailto:[email protected]>> on behalf of Timothy Coalson <[email protected]<mailto:[email protected]>> Date: Monday, February 1, 2016 at 12:46 AM To: Stephen Smith <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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<tel:%2B44%20%280%29%201865%20222726> (fax 222717) [email protected]<mailto:[email protected]> http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet<http://smithinks.net> _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[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. 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
