[HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-08-31 Thread Gopalakrishnan, Karthik
Hi all, I ran probtrackx for HCP subject 100206 using the MMP1.0 Glasser surface ROIs. My seeds in each ROI are at the white matter-gray matter boundary. I ran probtrackx in network mode as well as seed-to-ROI mode for the subject, and I applied the method described in http://journal.frontier

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] probtrackx network with HCP data and MMP parcellation Hi all, I ran probtrackx for HCP subject 100206 using the MMP1.0 Glasser surface ROIs. My seeds in each ROI are at the white matter-gray m

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
[HCP-Users] probtrackx network with HCP data and MMP parcellation Can you post your probtrackx call? Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Gopalakrishnan, Karthik" mailto:gkart...@gatech.edu>> Date: Thursday, August 31, 201

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Hi Matt, Here's the probtrackx calls: For network mode: probtrackx2 --network -x white-masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 500

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
@humanconnectome.org Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation What is in the .txt? Peace, Matt. From: "Gopalakrishnan, Karthik" mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:04 PM To: Matt Glasser mailto:glass...@wustl.ed

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
p-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation The file white-masks.txt and the file targets.txt contain newline-separated paths to each of t

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Which white matter surface are those on? I assume the bedpostX data are what we released? Peace, Matt. From: "Gopalakrishnan, Karthik" mailto:gkart...@gatech.

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
anconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Yes, I used the released bedpostX data. The white matter surfaces used were: 100206.L.white_MSMAll.32k_fs_LR.surf.gii 100206.R.white_

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
@humanconnectome.org Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Are all of these files in ${StudyFolder}/${Subject}/T1w? Matt. From: "Gopalakrishnan, Karthik" mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:19 PM To: Matt Glas

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
ass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Yes, both surface files I mentioned previously are the ones t

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Stamatios Sotiropoulos
stl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Yes, both surface files I mentioned previously are the ones that are provided in the fo

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
3:27 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Yes, both surface files

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Glasser, Matthew
stl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation S.O.S diffusion guys, poor and highly stressed Computer Science

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
stl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Yes, both surface files I mentioned previously are the ones that are pro

Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation

2017-09-01 Thread Gopalakrishnan, Karthik
4 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation S.O.S diffusion guys, poor and hi