Re: [HCP-Users] Where is nodif_brain for Diffusion? (FDT registration / PROBTRACKX)

[Glasser, Matthew]

Is there any reason that nodif_brain is needed for anything if nodif_brain_mask exists?  That is why we didn’t include it. Peace, Matt. From: Saad Jbabdi <saad.jba...@ndcn.ox.ac.uk> Date: Tuesday, July 1, 2014 at 3:09 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Where is nodif_brain for Diffusion? (FDT registration / PROBTRACKX) Hi You can easily create the nodif_brain image yourself with the FSL tools. For example: fslroi data nodif 0 1   (assuming the first volume is a b=0, which it is in the HCP data) fslmaths nodif -mas nodif_brain_mask nodif_brain However, note that the HCP diffusion data are resampled in T1w space as part of the preprocessing. So if your seed ROIs are in that space you don’t need to provide any transformation to probtrackx. Also, if your seed ROIs are in MNI space, then you can use the transformations provided by the HCP, which are in <subject>/MNINonLinear/xfms Cheers Saad On 1 Jul 2014, at 08:36, Linden Parkes <linden.par...@monash.edu> wrote: Hi, I'm trying to use FSL FDT to do some probabilistic tractography. I have run bedpostx and am now trying to run registration within FDT. According to an error I'm getting from the FSL FDT gui, I'm meant to have a nodif_brain image in the bedpostx directory but this is not the case. I do have the nodif_brain_mask image however. Am I missing something? Is this nodif_brain image meant to come with HCP datasets (e.g the new S500 release) or am I meant to create it myself? I can't see any mention of it in the S500 release reference manual. Or perhaps I shouldn't be using it at all? I figured I needed to use it in order to set the seed space to diffusion space. But if I'm wrong on this could someone tell me which file to use for the "seed to diff transform" and "diff to seed transform" in PROBTRACKX? Cheers, Linden _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466  (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi _______________________________________________ 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