Re: [HCP-Users] border file

The weights are to be able to place the border point somewhere other than at a vertex. The three vertices are one of the triangles in the surface file, and the weights represent where to place the point on that triangle. If you want a border point at a vertex, the weight for that vertex should

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Surface-based methods may boost your statistical power enough (by better alignment, exclusion of irrelevant tissue, and smoothing that doesn't cross sulcal banks, if you decide you need smoothing) that you may not need to rely as much on existing ROIs. Parcel-based statistics have a lot of power,

[HCP-Users] border file

Hi All, It seems that each vertex in the border files has an associated weight. What is this weight? If I want to draw a border vertex by vertex, how should I use the weights? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

Thanks, Tim, I'll try that and let you know if it worked. On Sat, Feb 24, 2018 at 12:21 AM, Timothy Coalson wrote: > The error message appears to be from syntax in a bash script, so it should > be possible to track it down. > > If you put "set -x" at the top of the script it

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

The error message appears to be from syntax in a bash script, so it should be possible to track it down. If you put "set -x" at the top of the script it fails in and rerun it, it will tell you each command before executing it, which should help narrow down which line is the problem. If the line

Re: [HCP-Users] wb_view crashes after 1 day of using it

Hello, Is wb_view crashing when loading a file or when you are performing an operation, perhaps editing annotations? John > On Feb 23, 2018, at 12:20 PM, Marta Moreno wrote: > > Dear experts, > > My wb_view crashes after 1 day of using it, what happens is that the

Re: [HCP-Users] wb_view crashes after 1 day of using it

Hi, I keep wb_view open for a long time and don¹t observe this behavior. If you can reproduce the crash and make a scene of it we could take a look. Matt. On 2/23/18, 12:20 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marta Moreno"

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

Alright, thank you! Darko On Fri, Feb 23, 2018 at 6:20 PM, Glasser, Matthew wrote: > No we don’t use python in that pipeline. I am afraid that no one else has > reported this and so I think the issue must be unique to your system. You > might trying on another computer/or

[HCP-Users] wb_view crashes after 1 day of using it

Dear experts, My wb_view crashes after 1 day of using it, what happens is that the next day I cannot keep loading more images with setting created for illustration of brain results and need to restart all over -even it requires to restart the computer to have it working properly. I have

Re: [HCP-Users] How to deal with the slight delay in 7 HCP Eprime tasks

There is no difference between the duration of the E-Prime tasks and the duration of the BOLD time series from the scan. There is likely a misunderstanding of what the duration should be, but I can’t help without knowing specifically what doesn’t line up in your opinion. There have been two

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

For a “recommended” analysis the only timeseries file you need is ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii. Peace, Matt. From: "Harms, Michael" > Date: Friday, February 23, 2018 at

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

No we don’t use python in that pipeline. I am afraid that no one else has reported this and so I think the issue must be unique to your system. You might trying on another computer/or in a VM where you install stuff from scratch and see if the issue persists. Peace, Matt. From: Darko

Re: [HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Hi Mike, We have a preprint out on this exact question and the conclusion is that it is really hard to do this accurately for most brain regions: https://www.biorxiv.org/content/early/2018/01/29/255620 Really the best idea is probably to go back and reanalyze the old data without volume-based

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

The FIX cleaned files have “clean” in their file name. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

Was the MSMAll one cleaned? Thanks Ze On Fri, Feb 23, 2018 at 9:43 AM, Harms, Michael wrote: > I guess, if you never plan on using the MSMSulc registered output from the > preprocessing output. But the CIFTI files are small compared to the volume > files, so I wouldn’t.

[HCP-Users] Best Approach for using old volumetric data to pick parcels-of-interest

Hi everyone, There's been a lot posted here over the past year or two on the challenges and limitations of going back-and-forth between volumetric space and HCP-defined surface space, with solid arguments for moving to (and sticking with) CIFTI-defined brainordinates. Here, I'm asking a

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

I guess, if you never plan on using the MSMSulc registered output from the preprocessing output. But the CIFTI files are small compared to the volume files, so I wouldn’t. Also, if you haven’t already cleaned the data (using FIX), you’ll need that file. -- Michael Harms, Ph.D.

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

Thanks Michael and Matt. Does that mean I can delete rfMRI_REST1_LR_Atlas.dtseries.nii to save some space? Ze On Thu, Feb 22, 2018 at 7:18 PM, Glasser, Matthew wrote: > These are both aligned to the FS_LR spherical surface geographic > convention. > > Peace, > > Matt. > >

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

Hi Matt, Yes, I believe so. It is the FreeSurfer 5.3.0-HCP. I also downloaded the latest version of that script and compared it with the one I have in my Pipelines folder and they seem identical. Could it maybe be python issue? Is FreeSurferHighResWhite written in python2? Because I had some

[HCP-Users] How to deal with the slight delay in 7 HCP Eprime tasks

Dear HCP experts, This is Meizhen Han from Peking University. Thanks for releasing the 7 fMRI tasks written in Eprime software used in Main HCP. I downloaded and run them on the Sinorad fMRI Stimili System in our lab. I find there is a slight difference between the actual time duration and