Re: [HCP-Users] run-level (level 1） functional MRI data

No. Those native.func.gii files are not what you want. We didn’t release the Level 1 task processing because we considered them “intermediate” files that would not be needed, or of much interest to others. What are you wanting to do with them? cheers, -MH -- Michael Harms, Ph.D.

[HCP-Users] GIFTI surface data

Hi, I use the lifespan rfMRI data. After preprocessing, there is a file in /subject/MNINonLinear/Results/rfMRI_REST1_LR named rfMRI_REST1_LR.L.native.func.gii with size, for example, 130576*420. Is this file the cortical BOLD signal time series data? Can I use it to do rfMRI analysis? Thanks.

Re: [HCP-Users] Overlaying atlas in Connectome Workbench

It is not for each individual and it is in MNI space. All I want to do is overlay the NIFTI onto a surface in MNI space. Thanks! Zach From: Glasser, Matthew Sent: Tuesday, May 23, 2017 1:31 PM To: Zachary Monge; NEUROSCIENCE tim Cc:

Re: [HCP-Users] Overlaying atlas in Connectome Workbench

Is this a NIFTI file in each individual subject or a group average NIFTI file? There isn’t a great way for mapping from group average NIFTI to surface, as the group averaging process causes a lot of blurring across subjects all over the cortex and also group average surfaces have their own

Re: [HCP-Users] Overlaying atlas in Connectome Workbench

Hi Tim, Thanks for the clarification! As of now my atlas is a nifti file. How can I create gifti label files from a nifti file? Sorry if this has been posted in the past... Sincerely, Zach From: Timothy Coalson Sent: Friday, May 19, 2017

Re: [HCP-Users] Incomplete diffuson datasets

Why would you only want to use b1000 scans? Those have less contrast for tractography. Peace, Matt. From: Ariana Cahn > Date: Tuesday, May 23, 2017 at 11:10 AM To: Matt Glasser > Subject: Re: [HCP-Users]

Re: [HCP-Users] Incomplete diffuson datasets

What is b1000 tractography and why would you want to do that? Peace, Matt. From: Ariana Cahn > Date: Tuesday, May 23, 2017 at 11:06 AM To: Matt Glasser > Subject: Re: [HCP-Users] Incomplete diffuson

Re: [HCP-Users] Incomplete diffuson datasets

Why not use all of the diffusion data that is present? Peace, Matt. From: > on behalf of Ariana Cahn > Date: Tuesday, May 23, 2017 at 10:59 AM To:

[HCP-Users] Incomplete diffuson datasets

Hello, I was wondering if it is still appropriate to perform b1000 tractography on incomplete diffusion datasets. I noticed there are files missing, and I'm just wondering which ones they are. Thanks, -- *Ariana Cahn* *BSc (Hons), *Neuroscience *ac...@ualberta.ca *

Re: [HCP-Users] run-level (level 1） functional MRI data

Hi, Do you want the “Level 1” results processed through the task model (GLM)? Or, do you just want the “minimally preprocessed” data that entered into the task analysis scripts? These are available in:

[HCP-Users] run-level (level 1） functional MRI data

Dear Professors, I want to use run-level data to do some analysis, and I wonder would file named *.native.fun.gii (e.g., tfMRI_WM_LR.L.natiive.func.gii) contains run-level functional data? Best, Jiang Jian - Graduate Student Beijing Normal University,

Re: [HCP-Users] Question about DWI protocol

Yes, in DiffPreprocPipeline_PostEddy.sh you’ll need to use “--combine-data-flag=2” Also, I want to caution you about collecting only half of the total dMRI data that we collected in the UMN Lifespan piloting. There is a reason that we collected a full 20 min of dMRI when using 1.5 mm

Re: [HCP-Users] Question about DWI protocol

Yes as long as you have phase reversed b0s you can have the DWIs have unique directions. The HCP diffusion pipeline might need modification to accommodate that. Peace, Matt. From: > on behalf of HMZ

Re: [HCP-Users] Subject keys

Yes, you can use the subject IDs in a public document, PROVIDED that NOTHING that comes from the RESTRICTED data is associated with that subject ID in your public document. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the

Re: [HCP-Users] cifti MATLAB

Hi, Are you using the latest gifti library available via the link mentioned here? https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? cheers, -MH -- Michael Harms, Ph.D. ---

Re: [HCP-Users] Group comparison of Myelin maps

Hi Donatas, The surface file, that correspond to one particular subject, is probably fine as far as it has the same geometry (number of vertices and faces) as all other subjects. For the area file, PALM expects it to be the average area across all subjects, as opposed to the actual areas for all

[HCP-Users] cifti MATLAB

Hi, There's something wrong when I load the cifti dense timeseries file into matlab. >> which ciftiopen /home/Tianjie/cifti/ciftiopen.m >>cii=ciftiopen('/home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_stru cture_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_A

[HCP-Users] Subject keys

Dear HCP-users, Is it allowed to use the original HCP subject keys in public documents? (I do not use the restricted data). Thanks and kind regards, Rikkert Hindriks ___ HCP-Users mailing list HCP-Users@humanconnectome.org

[HCP-Users] Question about DWI protocol

Dear HCP experts, This is Meizhen Han from Center for MRI research at Peking University in China. I'm writing for seeking a solution for the problem we encountered during the application of HCP MRI sequence on our recent research. I noticed that HCP acquired DWI data twice with reversed