Re: [HCP-Users] question about noise components in PTN release

[Stephen Smith]

Hi that’s right in the most recent PTN release the number of “junk” components 
is much lower, and also less unambiguously junk- so at this point we have not 
tried to classify them  
Cheers 


Stephen M. Smith,  Professor of Biomedical Engineering
Head of Analysis,   Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington,
Oxford. OX3 9 DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.uk
http://www.fmrib.ox.ac.uk/~steve
--

> On 16 May 2018, at 23:03, Glasser, Matthew  wrote:
> 
> I don’t think these were the same components.  There are probably a couple of 
> noise components in the PTN release but I don’t know if anyone went through 
> and numbered them.  
> 
> Peace,
> 
> Matt.
> 
> From:  on behalf of "Shearrer, Grace" 
> 
> Date: Wednesday, May 16, 2018 at 1:58 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] question about noise components in PTN release
> 
> Hello all, 
> a graduate student and I are working on an analysis with the 100 
> dimensionality PTN release. We are a bit confused about noise components in 
> the 100 dim PTN release. In the Smith et al. 2013 neuroimage paper it 
> mentions  that 78 of the 100 components were signal, and 22 were noise. 
> However, I cannot figure out which are signal or noise from the paper as it 
> appears to re-number the components for the figures. 
> 
> Is there a list of the 22 noise components in the 100 dimensionality PTN 
> release as mentioned in Smith et al 2013? 
> 
> I would like to ignore those noise components as suggested here 
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide.
> 
> Thank you,
> Grace
> 
> PS: I realize I could examine by hand which is noise or signal but that seems 
> redundant if someone already has
> 
> Grace Shearrer, PhD
> Post Doctoral Researcher
> Neuropsychology of Ingestive Behavior Lab 
> University of North Carolina Chapel Hill
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> 

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Re: [HCP-Users] CSF and WM masks

[Glasser, Matthew]

That is correct.  We don’t recommend WM and CSF regression necessarily, as it 
doesn’t do much (when the masks are eroded by 2 2mm voxels from the greymatter 
as these are).  If they are not eroded they behave more like global signal 
regression, which is controversial for removing a portion of the neural signal.

Peace,

Matt.

From: 
>
 on behalf of Thomas Arnold 
>
Date: Wednesday, May 16, 2018 at 12:39 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] CSF and WM masks

Greetings,

I'm looking to download the CSF and WM mask nifti files to be used in a 
regression. I've looked through the HCP release documentation and manually 
inspected the images I suspect to be the masks, but would appreciate 
confirmation that I've located the correct files.

The files I've located can be accessed through the following paths:
https://hcp-openaccess.s3.amazonaws.com/HCP_1200/100307/MNINonLinear/ROIs/CSFReg.2.nii
https://hcp-openaccess.s3.amazonaws.com/HCP_1200/100307/MNINonLinear/ROIs/WMReg.2.nii

If these aren't the correct files, I would greatly appreciate the path to the 
proper masks.

Thank you.

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Re: [HCP-Users] question about noise components in PTN release

[Glasser, Matthew]

I don’t think these were the same components.  There are probably a couple of 
noise components in the PTN release but I don’t know if anyone went through and 
numbered them.

Peace,

Matt.

From: 
>
 on behalf of "Shearrer, Grace" 
>
Date: Wednesday, May 16, 2018 at 1:58 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] question about noise components in PTN release


Hello all,

a graduate student and I are working on an analysis with the 100 dimensionality 
PTN release. We are a bit confused about noise components in the 100 dim PTN 
release. In the Smith et al. 2013 neuroimage paper it mentions that 78 of the 
100 components were signal, and 22 were noise. However, I cannot figure out 
which are signal or noise from the paper as it appears to re-number the 
components for the figures.


Is there a list of the 22 noise components in the 100 dimensionality PTN 
release as mentioned in Smith et al 2013?


I would like to ignore those noise components as suggested here 
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/DualRegression/UserGuide.

Thank you,
Grace


PS: I realize I could examine by hand which is noise or signal but that seems 
redundant if someone already has


Grace Shearrer, PhD
Post Doctoral Researcher
Neuropsychology of Ingestive Behavior Lab
University of North Carolina Chapel Hill

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[HCP-Users] CSF and WM masks

[Thomas Arnold]

Greetings,

I'm looking to download the CSF and WM mask nifti files to be used in a
regression. I've looked through the HCP release documentation and manually
inspected the images I suspect to be the masks, but would appreciate
confirmation that I've located the correct files.

The files I've located can be accessed through the following paths:
https://hcp-openaccess.s3.amazonaws.com/HCP_1200/100307/MNINonLinear/ROIs/CSFReg.2.nii
https://hcp-openaccess.s3.amazonaws.com/HCP_1200/100307/MNINonLinear/ROIs/WMReg.2.nii

If these aren't the correct files, I would greatly appreciate the path to
the proper masks.

Thank you.

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Re: [HCP-Users] Age problem

[Elam, Jennifer]

Hi Felix,

Access to exact age data for HCP subjects requires approval for Restricted Data 
access which can be applied for with this form: 
https://www.humanconnectome.org/storage/app/media/data_use_terms/DataUseTerms_HCP_RestrictedAccess_30Nov2017.pdf


Once you have access, you can download the Restricted CSV file from 
ConnectomeDB as described on pp. 25-27 of the S1200 Reference 
Manual.


The HCP young adult study included twins and their families and the MEG 
subjects were mostly twin pairs, so exact ages are considered potentially 
identifying. Users may also need to consider family structure in their analyses 
since many subjects are related and many traits are heritable.


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 Felix Yuan 

Sent: Wednesday, May 16, 2018 3:13:05 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Age problem


Dear HCP experts,

I am doing statistics analysis of MEG data.

And now in my processing steps, I really need the precise age of MEG subjects.

But in the downloaded data, I did not find any precise ages for all the 
subjects, only the range of age, like 22-25, 26-30, 31-35.

I want to know where can I get the precise age of HCP MEG subjects? Or can you 
send me the age files?



Thank you for your attention.

Best wishes,

Felix

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[HCP-Users] Age problem

[Felix Yuan]

Dear HCP experts,
I am doing statistics analysis of MEG data.
And now in my processing steps, I really need the precise age of MEG subjects.
But in the downloaded data, I did not find any precise ages for all the 
subjects, only the range of age, like 22-25, 26-30, 31-35.
I want to know where can I get the precise age of HCP MEG subjects? Or can you 
send me the age files?

Thank you for your attention.
Best wishes,
Felix

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