Hi Stam and Matt, I have one more question about this. I got the dense connectome and would like to calculate structural connectivity between the parcels in Matt's 360-parcel parcellation scheme. For the connectivity between parcel A and B, in the dense connectome matrix, I first located the rows belonging to A and the columns belonging to B, and then summed up the values in this submatrix. I used this summed value as the connectivity between parcel A and B. Would this make sense? Thank you.
Aaron ________________________________ From: Stamatios Sotiropoulos <stamatios.sotiropou...@nottingham.ac.uk> Sent: Wednesday, May 1, 2019 7:05 PM To: Glasser, Matthew Cc: Aaron C; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome This may be the reason indeed. The Pretractography script creates both native space and MNI space ROIs. You need to make sure you use the MNI ones (I.e. created via the MakeTrajectorySpace_MNI.sh script). Stam On 1 May 2019, at 23:52, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Is that because this is a native space grayordinates instead of an MNI space grayordinates and thus the masks are subject specific? Matt. From: Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> Date: Wednesday, May 1, 2019 at 12:27 PM To: Stamatios Sotiropoulos <stamatios.sotiropou...@nottingham.ac.uk<mailto:stamatios.sotiropou...@nottingham.ac.uk>> Cc: 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] Probabilistic tractography for dense connectome Hi Stam, I tried your PreTractography script to generate these files needed for probtrackx2, and then used the following command (the command from the HCP course for generating dense connectome): probtrackx2_gpu --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=Connectomes/stop --wtstop=Connectomes/wtstop \ --waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \ -x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \ --target3=Connectomes/Grayordinates.txt --dir=Connectomes The command completed without error. I then used the MATLAB to load the connectivity matrix: x=load(''fdt_matrix3.dot'); M=spconvert(x); However, the dimension of M is only 86392 x 86392, not 91282 x 91282. So I tried the same probtrackx2 command, but instead used the files from the HCP course virtual machine for the input to probtrackx2 (so this time I know the input files should be correct), but the dimension is still 86392 x 86392, not 91282 x 91282. If possible, would you please give me some hints to find out the missing grayordinates in this connectivity matrix? Thank you! Aaron ________________________________ From: Stamatios Sotiropoulos <stamatios.sotiropou...@nottingham.ac.uk<mailto:stamatios.sotiropou...@nottingham.ac.uk>> Sent: Friday, April 26, 2019 10:58 AM To: Aaron C Cc: Glasser, Matthew; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome 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. ________________________________ 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
