[HCP-Users] completely processed HCP data

[Bo Xu]

Is there anywhere a database of structural connectomes (SCs) and functional
connectomes (FCs) generated from HCP data? I mean, HCP publishes the raw
RMI images and pre-processed RMI images, but doesn't look like it publishes
completely processed data (e.g., the SCs and FCs for the 1200 subjects).
Wouldn't it make researchers' life much easier if someone generates the SCs
and FCs for 1200 subjects and put them somewhere for public access? If
there is no such thing, why? Is it because the neuroscience community
considers it trivial to generate SCs and FCs from pre-processed data (I'm
from the computer science community)? Or is it because researchers
typically wish to customize their specifications for SCs and FCs (e.g.,
parcellation, or cutoff value for terminating tracks)?

Thanks,
Bo

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Re: [HCP-Users] Bias Field setting in Resting State Stats script

[Glasser, Matthew]

What setting did you use in fMRIVolume?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Andrew Poppe mailto:poppe...@gmail.com>>
Date: Wednesday, September 5, 2018 at 4:35 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Bias Field setting in Resting State Stats script

Hello all,

I'm working on running the resting state stats batch script on our own data, 
and I am a bit stuck on what to set the bias field setting to. Based on the 
comments in the code as well as the code itself I think I have a general idea 
of what it's doing, but I wanted to specifically ask since I'm not 100% on what 
the setting should be. Could you briefly explain what the options represent?

Thanks a lot!

Andrew Poppe, Ph.D.
Postdoctoral Researcher
Olin Neuropsychiatry Research Center
Institute of Living
Hartford Hospital

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[HCP-Users] Bias Field setting in Resting State Stats script

[Andrew Poppe]

Hello all,

I'm working on running the resting state stats batch script on our own
data, and I am a bit stuck on what to set the bias field setting to. Based
on the comments in the code as well as the code itself I think I have a
general idea of what it's doing, but I wanted to specifically ask since I'm
not 100% on what the setting should be. Could you briefly explain what the
options represent?

Thanks a lot!

Andrew Poppe, Ph.D.
Postdoctoral Researcher
Olin Neuropsychiatry Research Center
Institute of Living
Hartford Hospital

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[HCP-Users] Software Versions for running HCP pipeline scripts

[Rutherford, Saige]

Hello,

The software version requirements for the HCP pipeline scripts available via 
GitHub are unclear. The pipeline scripts have been updated very recently (a few 
days ago), but the documentation on software requirements was last updated in 
2015 and does not cover if the required versions of FSL, FreeSurfer, and 
Connectome Workbench have changed. Could someone please confirm which versions 
of these software I need to have installed in order to run the HCP pipeline?

Thanks,
Saige


Saige E. Rutherford

Data Analyst // Research Assistant

Sripada Lab

Department of Psychiatry, University of Michigan

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Re: [HCP-Users] about the tfMRI

[Elam, Jennifer]

"TOM" stands for Theory of Mind or a mental interaction. Here's the info in the 
Reference Manual 

 (p. 52) on the social task:

Social Cognition (Theory of Mind)
Participants were presented with short video clips (20 seconds) of objects 
(squares, circles, triangles) that either interacted in some way, or moved 
randomly on the screen. These videos were developed by either Castelli and 
colleagues (Castelli et al. 2000) or Martin and colleagues (Wheatley et al. 
2007). After each video clip, participants judge whether the objects had a 
mental interaction (an interaction that appears as if the shapes are taking 
into account each
other’s feelings and thoughts), Not Sure, or No interaction (i.e., there is no 
obvious interaction between the shapes and the movement appears random). Each 
of the two task runs has 5 video blocks (2 Mental and 3 Random in one run, 3 
Mental and 2 Random in the other run) and 5 fixation blocks (15 seconds each).

Best,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of 罗 <963619...@qq.com>
Sent: Tuesday, September 4, 2018 4:22:27 AM
To: hcp-users
Subject: [HCP-Users] about the tfMRI

Dear professors:
In the tfMRI ALLTASKS zstatl, two blocks are in the 'Social' task: RANDOM and 
TOM, what is the detailed meaning of 'TOM'?
Thanks and best wishes!

发自我的iPhone

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[HCP-Users] about the tfMRI

[??]

Dear professors:
In the tfMRI ALLTASKS zstatl, two blocks are in the 'Social' task: RANDOM and 
TOM, what is the detailed meaning of 'TOM'?
Thanks and best wishes!


iPhone
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