Re: [HCP-Users] Expected date of 1,200 subjects release?

[David Van Essen]

Karthik,

We’re aiming for late this week, but if last-minute glitches arise it might 
stretch into next week.

David

> On Feb 20, 2017, at 1:33 PM, Gopalakrishnan, Karthik  
> wrote:
> 
> Hi Jenn,
>  
> Have any last-minute issues come up or is the S1200 release including the 
> bedpostx data going to happen this week?
>  
> Thanks!
> Karthik
>  
> From: hcp-users-boun...@humanconnectome.org 
>  
> [mailto:hcp-users-boun...@humanconnectome.org 
> ] On Behalf Of Elam, Jennifer
> Sent: Monday, February 13, 2017 11:07 AM
> To: Xavier Guell Paradis >; 
> hcp-users@humanconnectome.org 
> Subject: Re: [HCP-Users] Expected date of 1,200 subjects release?
>  
> Hi Xavier,
> The 1200 Subjects Release will include the per subject, across run level 2 
> results of the HCP task analysis processing pipeline. The level 3 group 
> average results will come later in a S1200 group average release once that 
> analysis is done.
>  
> 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: Xavier Guell Paradis >
> Sent: Saturday, February 11, 2017 1:34:19 PM
> To: Elam, Jennifer; hcp-users@humanconnectome.org 
> 
> Subject: RE: Expected date of 1,200 subjects release?
>  
> Dear Jenn,
> Thank you for your reply. Will this release include all level 2 and level 3 
> analyses, or only the preprocessed or raw data of the individual subjects?
> Thank you,
> Xavier.
> From: Elam, Jennifer [e...@wustl.edu ]
> Sent: Saturday, February 11, 2017 1:12 PM
> To: Xavier Guell Paradis; hcp-users@humanconnectome.org 
> 
> Subject: Re: Expected date of 1,200 subjects release?
> 
> Hi Xavier, 
> Look for it in the next week or two, barring any last minute issues. 
> 
> 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 Xavier Guell 
> Paradis >
> Sent: Saturday, February 11, 2017 9:07:07 AM
> To: hcp-users@humanconnectome.org 
> Subject: [HCP-Users] Expected date of 1,200 subjects release?
>  
> Dear HCP tema,
> Is there an expected date for the release of the 1,200 subjects data?
> Thank you very much,
> Xavier.
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> 
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> 
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> 

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Re: [HCP-Users] 2016 Course Material Download

[Elam, Jennifer]

Hi Tim,

PDFs of the lectures and practical instructions are now available on the 2016 
Course 
website.
 Competing priorities have delayed the release of a 2016 virtual machine with 
all the software and data used in the practicals. Hopefully, that will be 
available within a few weeks. We will announce it on the list when it is 
available.


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 Timothy Hendrickson 

Sent: Monday, February 20, 2017 1:37:38 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] 2016 Course Material Download

Hello,

I am curious when I can expect the 2016 Course Material tutorial data to be 
available for download?

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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[HCP-Users] 2016 Course Material Download

[Timothy Hendrickson]

Hello,

I am curious when I can expect the 2016 Course Material tutorial data to be
available for download?

Respectfully,

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

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Re: [HCP-Users] Expected date of 1,200 subjects release?

[Glasser, Matthew]

It will happen when it happens…

Peace,

Matt.

From: 
>
 on behalf of "Gopalakrishnan, Karthik" 
>
Date: Monday, February 20, 2017 at 1:33 PM
To: "Elam, Jennifer" >, Xavier Guell 
Paradis >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Expected date of 1,200 subjects release?

Hi Jenn,

Have any last-minute issues come up or is the S1200 release including the 
bedpostx data going to happen this week?

Thanks!
Karthik

From: 
hcp-users-boun...@humanconnectome.org
 [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Elam, Jennifer
Sent: Monday, February 13, 2017 11:07 AM
To: Xavier Guell Paradis >; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Expected date of 1,200 subjects release?


Hi Xavier,

The 1200 Subjects Release will include the per subject, across run level 2 
results of the HCP task analysis processing pipeline. The level 3 group average 
results will come later in a S1200 group average release once that analysis is 
done.



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: Xavier Guell Paradis >
Sent: Saturday, February 11, 2017 1:34:19 PM
To: Elam, Jennifer; 
hcp-users@humanconnectome.org
Subject: RE: Expected date of 1,200 subjects release?

Dear Jenn,
Thank you for your reply. Will this release include all level 2 and level 3 
analyses, or only the preprocessed or raw data of the individual subjects?
Thank you,
Xavier.

From: Elam, Jennifer [e...@wustl.edu]
Sent: Saturday, February 11, 2017 1:12 PM
To: Xavier Guell Paradis; 
hcp-users@humanconnectome.org
Subject: Re: Expected date of 1,200 subjects release?
Hi Xavier,
Look for it in the next week or two, barring any last minute issues.

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 Xavier Guell Paradis >
Sent: Saturday, February 11, 2017 9:07:07 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Expected date of 1,200 subjects release?

Dear HCP tema,
Is there an expected date for the release of the 1,200 subjects data?
Thank you very much,
Xavier.

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Re: [HCP-Users] Expected date of 1,200 subjects release?

[Gopalakrishnan, Karthik]

Hi Jenn,

Have any last-minute issues come up or is the S1200 release including the 
bedpostx data going to happen this week?

Thanks!
Karthik

From: hcp-users-boun...@humanconnectome.org 
[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Elam, Jennifer
Sent: Monday, February 13, 2017 11:07 AM
To: Xavier Guell Paradis ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Expected date of 1,200 subjects release?


Hi Xavier,

The 1200 Subjects Release will include the per subject, across run level 2 
results of the HCP task analysis processing pipeline. The level 3 group average 
results will come later in a S1200 group average release once that analysis is 
done.



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: Xavier Guell Paradis >
Sent: Saturday, February 11, 2017 1:34:19 PM
To: Elam, Jennifer; 
hcp-users@humanconnectome.org
Subject: RE: Expected date of 1,200 subjects release?

Dear Jenn,
Thank you for your reply. Will this release include all level 2 and level 3 
analyses, or only the preprocessed or raw data of the individual subjects?
Thank you,
Xavier.

From: Elam, Jennifer [e...@wustl.edu]
Sent: Saturday, February 11, 2017 1:12 PM
To: Xavier Guell Paradis; 
hcp-users@humanconnectome.org
Subject: Re: Expected date of 1,200 subjects release?
Hi Xavier,
Look for it in the next week or two, barring any last minute issues.

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 Xavier Guell Paradis >
Sent: Saturday, February 11, 2017 9:07:07 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Expected date of 1,200 subjects release?

Dear HCP tema,
Is there an expected date for the release of the 1,200 subjects data?
Thank you very much,
Xavier.

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Re: [HCP-Users] dMRI after eddy but before acpc-T1W

[Philip A Cook]

Hi,

I believe the unwarped eddy output will be under

Diffusion/eddy/eddy_unwarped_images.nii.gz

https://github.com/Washington-University/Pipelines/blob/6e22e45a066df542660ad0cdb2e1cec6a373ecb4/DiffusionPreprocessing/scripts/run_eddy.sh#L523



> On Feb 2, 2017, at 10:08 AM, Szabolcs David  wrote:
> 
> Hi All,
> 
> I would like to look at the eddy corrected diffusion images+bvecs, but before 
> the realignment to the T1w. Is it possible somehow?
> Or maybe just the trafo file of b0 to T1w registration available somewhere?
> 
> Cheers,
> Szabolcs
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> 


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Re: [HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

[Glasser, Matthew]

We have found that ICA+FIX does improve the HCP taskfMRI data.  It reduces 
false positives/false negatives in the beta maps and increases Z statistics.  
For short tfMRI runs, I would recommend combining across runs so that ICA+FIX 
can better separate signal and noise and so that the clean up regression is 
better conditioned.

Peace,

Matt.

From: 
>
 on behalf of "Poppe, Andrew" 
>
Date: Monday, February 20, 2017 at 9:28 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

Hello,

Our group is trying to decide if, and to what extent, using ICA-FIX improves 
GLM results in our data analysis. We analyzed the same data with the same 
models once using FIX prior to calculating stats and again without using FIX.

We want to know how we might compare the two.

One idea we had was to determine how well the model fit, as a reduction in 
noise in the data should hopefully produce a more consistent model fit.

To measure this, I tried to use the VARCOPEs associated with each COPE as a 
measure of variability of the model fit. However, because the scale of these 
images varied with the scale of the input data, I decided to divide each 
VARCOPE image by the variance-across-time of the input data, producing 
something like an R-squared image. Another method would be to calculate the 
variance of the res4d image and divide that by the total variance and then 
subtract from an image of all 1's. That should hopefully produce an R-squared 
for the entire GLM model, as opposed to an individual COPE.

I'm wondering if I'm fundamentally thinking about these images wrong, and 
especially if there is a better way to compare the two analysis streams. 
Without ground truth, is it possible to say whether FIX improved the analysis 
in a GLM framework?

Thanks,

Andrew Poppe, PhD
Olin Center
Institute of Living
Hartford Hospital

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Re: [HCP-Users] how to register the DTI T1 to the structure T1

[Glasser, Matthew]

Run the diffusion preprocessing pipeline.

Peace,

Matt.

From: 
>
 on behalf of *signal >
Date: Monday, February 20, 2017 at 8:45 AM
To: hcp-users 
>
Subject: [HCP-Users] how to register the DTI T1 to the structure T1

Thank you for your time,I download and release the HCP pipeline v3.21.0 and it 
can implement the "structure preprocessing" step.And now I want to know how to 
register the DTI T1 to  the structure T1.Where do I get the data?Your reply is 
highly appreciated.

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[HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

[Poppe, Andrew]

Hello,

Our group is trying to decide if, and to what extent, using ICA-FIX improves 
GLM results in our data analysis. We analyzed the same data with the same 
models once using FIX prior to calculating stats and again without using FIX.

We want to know how we might compare the two.

One idea we had was to determine how well the model fit, as a reduction in 
noise in the data should hopefully produce a more consistent model fit.

To measure this, I tried to use the VARCOPEs associated with each COPE as a 
measure of variability of the model fit. However, because the scale of these 
images varied with the scale of the input data, I decided to divide each 
VARCOPE image by the variance-across-time of the input data, producing 
something like an R-squared image. Another method would be to calculate the 
variance of the res4d image and divide that by the total variance and then 
subtract from an image of all 1's. That should hopefully produce an R-squared 
for the entire GLM model, as opposed to an individual COPE.

I'm wondering if I'm fundamentally thinking about these images wrong, and 
especially if there is a better way to compare the two analysis streams. 
Without ground truth, is it possible to say whether FIX improved the analysis 
in a GLM framework?

Thanks,

Andrew Poppe, PhD
Olin Center
Institute of Living
Hartford Hospital

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[HCP-Users] how to register the DTI T1 to the structure T1

[*signal]

Thank you for your time,I download and release the HCP pipeline v3.21.0 and it 
can implement the "structure preprocessing" step.And now I want to know how to 
register the DTI T1 to  the structure T1.Where do I get the data?Your reply is 
highly appreciated.
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