Hi Aaron You need the PreTractography script, available in one of the branches of the WU-pipelines.
https://github.com/Washington-University/HCPpipelines/tree/diffusion-tractography/DiffusionTractography Best wishes Stam On 26 Apr 2019, at 15:50, Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> wrote: Hi Matt, Thank you for letting me know. The full command I mentioned is as follows: probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged \ --mask=../T1w/Diffusion.bedpostX/nodif_brain_mask \ --xfm=xfms/standard2acpc_dc \ --invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz \ --loopcheck --forcedir -c 0.2 --sampvox=2 --randfib=1 \ --stop=Connectome/stop --wtstop=Connectome/wtstop \ --waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \ -x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \ --target3=Connectomes/GrayOrdinates.txt --dir=Connectomes It's in the HCP course practical "Fibre Orientation Models and Tractography Analysis" taught by Matteo Bastiani. Thank you. ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Thursday, April 25, 2019 7:04 PM To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Cc: Stamatios Sotiropoulos Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome Not as far as I am aware, but Stam might know. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Thursday, April 25, 2019 at 9:15 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Probabilistic tractography for dense connectome Dear HCP experts, I have a question about the probabilistic tractography command used for generating dense connectome (https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any shared scripts for generating "pial.L.asc", "white.L.asc", "Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as "CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography command? _______________________________________________ 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. This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
