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

Thanks a lot, Matt! I just saw Stam's email and responded as well. Regards, Karthik From: Glasser, Matthew Sent: Friday, September 1, 2017 5:07:25 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] probtrackx network with HCP

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

Hi Stam, Thanks for the suggestion! Is this only for the network mode call (corrected call pasted below)? probtrackx2 --network --omatrix1 --loopcheck -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 --

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" mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 4:04 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-u

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 lef

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

Hi Karthik You need to run —network —omatrix1, and I would add —loopcheck. Have a look at the HCP course tractography practical for the different options in getting connectomes. Cheers Stam On 1 Sep 2017, at 21:30, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I don’t immediately see a

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" mailto:gkart...@gatech.edu>> Date: Friday, September 1, 2017 at 3:27 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hc

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 Sent: Friday, September 1, 2017 4:21:43 PM To: Gopalakrishnan, Karthik; hcp-users@h

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 Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org" mailto:hcp-

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 Sent: Friday, September 1, 2017 4:14:03 PM To: Gopalakrishn

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.edu>> Date: Friday, September 1, 2017 at 3:11 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

Well, if they want to get to cifti starting from the volume data, I still wouldn't suggest -volume-parcel-resampling. Instead, just use the subject's subcortical label volume when making the initial flipped or not flipped cifti files, and use -cifti-resample to get them into a shared grayordinate

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 Sent: Friday, September 1, 2017 4:06:15 PM To: Gopalakrishnan, Karthik; hcp-users@humanconnectome.org

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.edu>>, "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

Mike was talking about the effect of using some within parcel smoothing and some between parcel smoothing so I suggested he make the data from scratch if he wants to do all between parcel smoothing. I think they should just smooth within parcels and only add the needed smoothing to get things u

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.

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

I missed an important word: in the second paragraph, it should read "...the ideal way would be to also create an X flipped subcortical *label* volume file, then swap left and right labels in it..." Tim On Fri, Sep 1, 2017 at 3:02 PM, Timothy Coalson wrote: > Using that transform that flips X a

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

Using that transform that flips X around the origin should put left on right and right on left, yes. Note, however, that the left and right parcel ROIs are not the same, so you will have to figure out how to handle the mismatched edges. I would not suggest -volume-parcel-resampling. If you want

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

I guess I don’t know why one would want to smooth across the known boundaries, but the option is available in wb_command -cifti-smoothing. One could instead redo the volume mapping to CIFTI with wb_command -volume-parcel-resampling using a very small number for the kernel, and then apply the ch

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

@Matt: The minimally preprocessed subcortical data in the CIFTI was smoothed with a 2 mm FWHM “parcel-constrained” kernel, right? (i.e, the smoothing does not cross boundaries of subcortical structures). In that case, if they were to then further smooth the subcortical data, but smooth across

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

1. That command for the surface is not quite what you are looking for. For the surface, the left and right hemisphere vertices are already in register (meaning that vertices with the same number will be in the anatomically corresponding location). You would need to translate between the CIFTI

Re: [HCP-Users] Question about restricted data

Hi Claude, Sorry that some of the variables don't have more logical scoring. The up to date HCP data dictionary with the following clarifications is available for download on the HCP wiki: https://wiki.humanconnectome.org/x/N4AvAw SSAGA_Agoraphobia is scored 1 = No agorophobia experienced over

[HCP-Users] clustering of subcortical structures - flipping and smoothing

Dear HCP list, We’re interested in clustering of subcortical structures in the HCP resting-state fMRI data and have two questions regarding the pre-processing: 1. We’re looking for a way to flip the data of the two hemispheres, including subcortical structures, It seems that an option exist to

Re: [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, 2017 at 9:27 PM To: "HCP-Users@humanconnectome.org" mailto