Thanks a lot, Matt! I just saw Stam's email and responded as well.
Regards, Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu> Sent: Friday, September 1, 2017 5:07:25 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Well the good news is that all of that looks correct and Stam made some concrete suggestions as to your probtrackx command. Peace, Matt. From: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 4:04 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] probtrackx network with HCP data and MMP parcellation S.O.S diffusion guys, poor and highly stressed Computer Science grad student here, trying to break into the neuroscience community! :) Matt, in case this helps, here are the commands I used to go from the released ROI files to the subject ROIs, in order: 1) Create .label.gii files from both left and right hemisphere ROI files. wb_command -cifti-separate Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Final_Final_Areas_Group.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_LEFT LEFT.label.gii wb_command -cifti-separate Q1-Q6_RelatedParcellation210.R.CorticalAreas_dil_Final_Final_Areas_Group.32k_fs_LR.dlabel.nii COLUMN -label CORTEX_RIGHT RIGHT.label.gii 2) Convert the .label.gii files to .func.gii files. wb_command -gifti-all-labels-to-rois LEFT.label.gii 1 LEFT.func.gii wb_command -gifti-all-labels-to-rois RIGHT.label.gii 1 RIGHT.func.gii 3) Break each .func.gii file into 180 .func.gii files, one for each ROI. wb_command -metric-merge left-roi-1.func.gii -metric LEFT.func.gii -column 1 (the above command is run 180 times, with -column ranging from 1 to 180 and the output file name being left-roi-<i>.func.gii where <i> ranges from 1 to 180; I repeated the same thing another 180 times to obtain right-ROIs as well) 4) Convert each .func.gii ROI file into subject .gii ROI file using surf2surf surf2surf -i <surface_file> -o left-roi-1.gii --values=left-roi-1.func.gii Here, <surface_file> is <subject_number>.L.white_MSMAll.32k_fs_LR.surf.gii for a left-hemisphere ROI and <subject_number>.R.white_MSMAll.32k_fs_LR.surf.gii for a right-hemisphere ROI. Now these .gii files are the ones I provide to probtrackx. Regards, Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:30:31 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation I don’t immediately see an issue with your calls to probtrackx, perhaps one of the diffusion guys will take a look and find something… Matt. From: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:27 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] probtrackx network with HCP data and MMP parcellation Yes, both surface files I mentioned previously are the ones that are provided in the following directory: ${Subject}/T1w/fsaverage_LR32k Thanks! Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:21:43 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org<mailto:hcp-users@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" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:19 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] 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_MSMAll.32k_fs_LR.surf.gii Thanks! Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:14:03 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org<mailto: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" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:11 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] 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 the 360 ROIs (.gii files). Thanks! Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 4:06:15 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation What is in the .txt? Peace, Matt. From: "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:04 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] 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 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s Diffusion.bedpostX/merged -m Diffusion.bedpostX/nodif_brain_mask.nii.gz --dir=WHITE_NETWORKMODE For seed-to-ROI mode (in this example, the seed ROI is L_1.gii, but I did this for all 360 ROIs): probtrackx2 --seed=../whiteROIs/L_1.gii -l -c 0.3 -S 2000 --steplength=0.3 -P 5000 --fibthresh=0.01 --distthresh=20.0 --forcedir --opd -s ../Diffusion.bedpostX/merged -m ../Diffusion.bedpostX/nodif_brain_mask --dir=L1 --targetmasks=targets.txt --os2t --s2tastext Thanks! Karthik ________________________________ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Friday, September 1, 2017 8:16:51 AM To: Gopalakrishnan, Karthik; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] probtrackx network with HCP data and MMP parcellation Can you post your probtrackx call? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Gopalakrishnan, Karthik" <gkart...@gatech.edu<mailto:gkart...@gatech.edu>> Date: Thursday, August 31, 2017 at 9:27 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <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 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.frontiersin.org/article/10.3389/fninf.2016.00046/full to infer structural networks from the resultant data from probtrackx. What I observe is that the networks aren't particularly dense. Since MMP1.0 has 360 ROIs, there are 360*359 = 129240 possible directed edges, but the networks I infer have about 2300 edges, which is a density of ~2%. Could someone share their insights on why I'm observing such low-density networks/where I might be doing something wrong? Thanks! Karthik _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
