I would separate the CIFTI file into GIFTI and NIFTI components with wb_command -cifti-separate and follow the instructions for surface tracking on FSL’s website.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:19 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation To Whom it may concern, I have created a dlabel file by adding to the Glasser Parcellation from BALSA the subcortical regions of the Freesurfer atlas. Now my goal would be to run a tractography analysis and obtain structural connectivity matrices using this cortical+subcortical parcellation. Could you suggest the simplest way to go from my dlabel file to something that is compatible with diffusion software? I know that probtrackx accepts GIFTIs as input, but I was wondering about how to extend this to subcortical areas. Or rather would the simplest solution be to convert each subject’s parcellation into a series of NIFTI files in native/standard space and input these as ROIs into probtrackx? In this case, could you recommend the correct series of workbench commands? I am also open to other software recommendations besides the FSL suite. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 _______________________________________________ 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
