You can use the nodif_brain_mask for this. As for questions about the FDT GUI, you will have to ask those on the FSL list as I am only familiar with the probtrackx command line.
Peace, Matt. From: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Wednesday, November 2, 2016 at 1:58 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data Many thanks Matt. I ran probtrackx with no XFM then. It seemed that probtrackx completed successfully, although I got this error at the very end: [cid:ADA2B284-976C-43DC-A8A3-0F49A79CD654] Any idea? From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Wednesday, November 2, 2016 at 2:30 PM To: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data No need for XFMs. Peace, Matt. From: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Wednesday, November 2, 2016 at 1:19 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data So just to see if I understood your point, If I use surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k for probtrackx, then there is no need to provide –xfm and —inxfm transform arguments? Or do I still need to run FNIRT between diffusion space and T1w and use the results in —xfm and —xfm arguments of probtrackx? From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:41 PM To: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data The MMP1.0 ROIs are not registered to a 3D average brain. They exist on a 2D standard surface mesh. I mention below the individual subject versions of this surface mesh that you could use for tractography. In that case, you would use the white matter surface as your waypoint and the pial surface as your stop. Peace, Matt. From: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Tuesday, November 1, 2016 at 6:39 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data My plan is indeed to run probtrackx using surface ROIs. But since HCP diffusion data is not registered to the average brain template of the MMP1.0 ROIs, my question is what is the recommended way of running FNIRT for doing so? What is the appropriate template file(T1w)? And is there any config file HCP releases to be used by FNIRT? From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:29 PM To: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data You can map the parcellation from the surface to the volume using the white and pial surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k and the ribbon-based option. Also, some tractography tools like probtrackx allow you to track directly to surface ROIs (which is better). Peace, Matt. From: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Tuesday, November 1, 2016 at 6:27 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data Hi Matt., Yes, It is an HCP subject. Thanks, Kamal From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, November 1, 2016 at 7:25 PM To: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] FNIRT for HCP diffusion data Is this an HCP subject or another subject? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Tuesday, November 1, 2016 at 12:18 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] FNIRT for HCP diffusion data Hi all, I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0 ROIs. To my understanding the corresponding T1w image of MMP1.0 ROIs is: HCP_PhaseTwo / Q1-Q6_RelatedParcellation210 / MNINonLinear / Q1-Q6_RelatedParcellation210_AverageT1w_restore.nii.gz Is this a right choice? Now I want to register a subject diffusion.bedpostx directory to the MMP1.0 ROI space using FNIRT. Is there an HCP config file for the FNIRT registration? If not any recommended settings? Any pointer is much appreciated. Thanks, Kamal Shadi _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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