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
