Re: [HCP-Users] Tractography on diffusion data for SC matrices

Hi Joelle and all, HCP does have running bedpostX on the diffusion data for HCP Subjects on our to do list, but this data has not been released yet. We are hoping to have this available to users by late winter/early spring 2016 after we release 7T data. Best, Jenn Jennifer Elam, Ph.D.

Re: [HCP-Users] Convert NIFTI to CIFTI

The -cift-convert command is only files that are organized the way cifti is - the data in question has to have already been in cifti space before using the command will do anything for you. The nifti files written and accepted by the command are "fake" nifti files, they only superficially

Re: [HCP-Users] Convert NIFTI to CIFTI

Yes, I have, like so: wb_command -cifti-convert -from-nifti ${NiftiIn} ${CiftiTemplate} ${CiftiOut} -reset-scalars But not in the context you describe. I was using randomise to generate group permuted t-maps and then bring them back to cifti before doing TFCE on the surface. (Now I use PALM

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

What CIFTI data are you trying to get into matlab? Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of David Dalmazzo Sent: Monday, November 23, 2015 11:18 AM To:

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Usually you concatenate them temporally after demeaning (and perhaps variance normalizing). Peace, Matt. From: hcp-users-boun...@humanconnectome.org on behalf of Joelle Zimmermann Sent:

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

Hi Matt, This file is HCP_S500_R468_MIGPd4500ROW.dconn.nii (33GB). But right now it is working with the last updated version of fieldtrip. Thanks for the support anyway David On Mon, Nov 23, 2015 at 7:14 PM, Glasser, Matthew wrote: > What CIFTI data are you trying to get

Re: [HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

To get a dconn loaded in matlab, you of course need to have a large amount of available memory. Freezing is what I would expect if you don't have enough memory, and start using a lot of swap space (some ways of loading might initially load it as double precision, and need twice the memory). As

Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

Hi Kevin, It's been more than two years and I am wondering if there has been any updates for downloading the HCP data via command line? Thanks, Cherry ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

It doesn't matter what order you concatenate the data in, but I would not recommend only analyzing the data of one phase encoding direction. Peace, Matt. From: > on behalf of Joelle Zimmermann

Re: [HCP-Users] aliasing in diffusion images

What are your settings on all the parameters on the Sequence:Special tab? --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box

Re: [HCP-Users] aliasing in diffusion images

Excite pulse duration: 2560 us Refocus pulse duration: 5120 us Single band images: off MB LeakBlock Kernel: off MB RF phase scramble: off Time-shifted MB RF: off SENSE1 coil combine: ON Log physiology to file: off Invert RO/PE polarity: off Online multi-band recon: Online FFT scale factor: 1.00

Re: [HCP-Users] Phase Encoding left-to-right and right-to-left

Hi Jennifer and Matt, Thanks for your help. I have a few clarification questions below: Does it matter in which order I concatenate the LR and the RL .nii's? My ultimate goal is to create a functional connectivity matrix from the time series. #3 in the link you sent describes that there are 4

[HCP-Users] Tractography on diffusion data for SC matrices

Hi Jennifer, I previously posted a question to the mailing list, and wanted to check with you as you may have a bit more of an insiders scoop. I was wondering whether tractography has been performed on the diffusion data for the end of creating structural connectivity matrices for individual

[HCP-Users] Convert NIFTI to CIFTI

Hi, I'm a PhD student just getting started on a project that involves analyzing some data from the 500 subjects release and wanted to know if anyone has had any experience using the *-cifti-convert -from-nifti *operations to make cifti files. Ultimately, the goal is to compare test-retest

[HCP-Users] Trying to read HCP_S500_R468_MIGPd4500ROW.dconn.nii

Hello, I work in Specs Lab in Pompeu Fabra University as a Phd student. I'm building an app for connectome visualisation and brain activity simulation called BrainX3. The first version use Hagmann dataset based on 998 nodes and ~14.000 bidirectional connections. For the new version I would like