Re: [HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

[Elam, Jennifer]

This has got to be a link from the Github Pipelines, right Vanessa?


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 Coalson 

Sent: Tuesday, June 18, 2019 1:23:54 PM
To: DE CASTRO Vanessa
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] problems to download the example data to run HCP 
Pipelines and NHPPipelines

Could you clarify what exactly you tried to download?  I don't know of any 
non-human data in connectomedb, either.

Tim


On Tue, Jun 18, 2019 at 9:17 AM DE CASTRO Vanessa 
mailto:vanessa.decas...@cnrs.fr>> wrote:
Good morning, I'm trying to download the example data to run the HCP Pipelines, 
and also the ones related to the non-human primates, and there is no way; even 
with the last version of Aspera Connect. What can I do? Than you very much.

Sincerely,

--

Vanessa DeCastro, PhD

Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
Pavillon Baudot CHU Purpan
31052 Toulouse Cedex 03, France


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Last weeks to register for HCP Course 2019!

[Elam, Jennifer]

Reminder that it's the last few weeks to register for this year's HCP Course 
July 8 – 12, 2019 in beautiful, cool Portland, Oregon. We have room for you! 
Don't delay, our hotel booking deadline is one week from today, Saturday June 
15.

Check out the updated HCP Course schedule and faculty 
list!

This year we have expanded our hands-on sessions to help you discover and use 
HCP neuroimaging analysis pipelines. Course attendees will even have the 
opportunity to try out and troubleshoot the HCP Pipelines out on their own data!

We're also covering the just released Lifespan HCP Development (ages 5-21) and 
Aging (ages 36-100+) data and updates to the suite of shared methods an tools 
developed by HCP that you can use in your work.
For more info visit the 

 HCP Course 2019 
website.
 Register soon, the course is filling up fast!

If you have any questions, please contact us at: 
hcpcourse@humanconnectome.org

We look forward to seeing you in Portland!
Best,
2019 HCP Course Organizers

P.S. If you are lucky enough to be attending OHBM in Rome this week, you can 
find out more about the HCP Course and the Brain Analysis Library of Spatial 
maps and Atlases (BALSA) data sharing platform at Table Top #1 (right by the 
bar)! Come see us!

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Item data for NIH Emotion battery

[Elam, Jennifer]

Hi Leonardo,

Do you mean the NIH Toolbox Emotion domain? I can send you the TB data as a 
spreadsheet off list.


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 Leonardo Tozzi 

Sent: Wednesday, May 29, 2019 1:45:44 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Item data for NIH Emotion battery


Dear Experts,



I would like to access the item-level data for the NIH Emotion battery of the 
young adult release.

How can I do that?
Thank you,





Leonardo Tozzi, MD, PhD

Williams PanLab | Postdoctoral Researcher

Stanford University | 401 Quarry Rd

lto...@stanford.edu | (650) 5615738



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Announcing HCP Lifespan Aging and Development Release 1.0!

[Elam, Jennifer]

Announcing the first data release from the Lifespan Human Connectome Projects 
on the NIMH Data Archive 
(NDA)!
 Data from two studies of healthy individuals are now available to authorized 
NDA users: HCP-Aging 
(HCP-A, ages 36-100+) and HCP 
Development 
(HCP-D, ages 5-21).


Lifespan HCP Release 1.0 Data includes unprocessed data of all modalities 
(structural MRI, resting state fMRI, task fMRI, and diffusion MRI) for 600+ 
subjects each from HCP-A and HCP-D and minimally preprocessed structural MRI 
data (only) for 129 HCP-A and 84 HCP-D subjects, respectively. Basic 
demographic information is also available on all released subjects. Because 
some subjects in these studies are related, unrelated datasets are available as 
shared packages or can be filtered on to create a custom package in NDA.


Read HCP Data Access 
Instructions
 for step-by-step instructions on obtaining the data. If you are new to the 
NDA, see below instructions.


Join us for HCP Course 
2019
 July 8-12 in Portland, Oregon, USA if you want to learn more about how to get 
the most out of Lifespan data and all about the tools and methods developed by 
the HCP.

Only a few weeks left to register!


If you don't currently have an account on the NDA, start the process by 
creating an NDA account.

Request access to the Lifespan HCP data by:

1. Log in and go to your Data 
Permissions dashboard.

2. Request Access to the Adolescent Brain and Cognitive Development (ABCD) 
permissions group.

3. Complete the access request instructions.

For detailed information on the process or criteria for access, visit Access 
Review.

** If you already have access to ABCD data, you only need to login to 
NDA
 to access Lifespan HCP data.


Stay tuned for future releases in the coming months for more processed Lifespan 
image and behavioral data on these subjects and hundreds more!


Best,

The Lifespan HCP Consortia and CCF Release Team

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] volumetric segmentation of subcortical structures

[Elam, Jennifer]

Hi Cecelia,

Did you sign the data Use Terms when you logged into ConnectomeDB after 
creating an account? If not, click the "Data Use Terms Required" button and 
sign the terms:

 [cid:e7cb7ff5-f8e5-478a-860e-3f22d19abde1]


After that, click Open Dataset  and it will take you to 
https://db.humanconnectome.org/data/projects/HCP_1200.

Look in the left column for “Quick Downloads” and find the “Expanded FreeSurfer 
Data” link.


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 Mazzetti, C. (Cecilia) 

Sent: Thursday, May 16, 2019 9:09:55 AM
To: Harms, Michael; Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] volumetric segmentation of subcortical structures


Thanks so much Michael,

That's indeed the only thing I need :)

I just made an account but I can't find the link you say (“quick download” ). 
could you maybe check if it's indeed in the link you pasted? Thanks in advance 
this would be very helpful!


Best,
Cecilia


Cecilia Mazzetti - Ph.D. Candidate
Donders Centre for Cognitive Neuroimaging, room 2.257
Kapittelweg 29 | 6525 EN Nijmegen


Da: Harms, Michael 
Inviato: giovedì 16 maggio 2019 15:51
A: Glasser, Matthew; Mazzetti, C. (Cecilia); hcp-users@humanconnectome.org
Oggetto: Re: [HCP-Users] volumetric segmentation of subcortical structures




Hi,

If you simply want all the FreeSurfer quantification in tabular form, you can 
select the “Expanded FreeSurfer Data” link under “Quick Downloads”, available 
here https://db.humanconnectome.org/data/projects/HCP_1200



(You will need a ConnectomeDB account).



Cheers,

-MH



--

Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu



From:  on behalf of "Glasser, Matthew" 

Date: Thursday, May 16, 2019 at 6:14 AM
To: "Mazzetti, C. (Cecilia)" , 
"hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] volumetric segmentation of subcortical structures



${StudyFolder}/${Subject}/MNINonLinear/wmparc.nii.gz in the structural packages.



Matt.



From:  on behalf of "Mazzetti, C. 
(Cecilia)" 
Date: Thursday, May 16, 2019 at 3:51 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] volumetric segmentation of subcortical structures



Dear all,

I am required to come up with a proof of concept for subcortical 
lateralizations found in my study. Ideally, consistent lateralizations derived 
from a. bigger dataset such as the HCP one, would do the job more than fine. A 
colleague told me there should be a file somewhere, with structural 
segmentation data (i.e., volumes) already done for the MRIs in the database. I 
am wondering whether someone knows if: 1. this is true, 2. if yes, is it 
possible to access? and how ?



Thanks very much in advance to anyone willing to help



Best,

Cecilia



​

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org

Re: [HCP-Users] Query regarding PSQI 'Other' scores

[Elam, Jennifer]

Hi Nicole,

Yes, we do have information that subjects provided in an open field (5j. 
Describe: ) for PSQI 5.During the past month, how often have you had trouble 
sleeping because of...  (j) Other reason(s), as described in 5j. pt2 0=Not 
during the past month, 1=Less than once a week, 2=Once or twice a week, 3=3 or 
more times a week


This information is not in a form that is easy to share at the moment and we 
are currently prioritizing the preparations for the upcoming HCP-Development 
and HCP-Aging Release 1.0 so it might take a few weeks to extract the data.


Are there particular subjects you are interested in or do you need this data on 
all subjects?


Thanks,

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 Nicole Kuek 

Sent: Wednesday, May 1, 2019 9:40:05 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Query regarding PSQI 'Other' scores

Dear HCP Experts,

Regarding the individual measure scores of 'PSQI_Other', was more specific 
information regarding what exactly these 'Other' disturbances were collected? 
If so, would it be possible to get this information?

--
Best Regards,

Nicole K.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] coding of videos in social task?

[Elam, Jennifer]

Hi David,

The A and B versions allowed for tasks to be rerun on a subject who had an 
issue with their "A" run without running the exact same version of the task 
(which would bias the subject's responses).


CCing Greg Burgess who can answer the question about the random condition.


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 David V. Smith 

Sent: Tuesday, April 30, 2019 10:12:35 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] coding of videos in social task?

Hi -- I was hoping to adapt the social task for another experiment, and I was 
wondering how the video stimuli were coded. I see that a couple of the files 
have "random" in the file name, but are these the only stimuli that would work 
for the "Random" condition? See below. Also, I'm assuming the "A" and "B" 
splits are linked to the fact that the original videos were pretty long and the 
HCP split them to make shorter blocks?

Thanks!
David


BILLIARD-A.AVI
BILLIARD-B.AVI
COAXING-B.AVI
DRIFTING-A.AVI
DRIFTING-B.AVI
Dancing.AVI
Fishing.AVI
MOCKING-A.AVI
MOCKING-B.AVI
Random mechanical.AVI
Random social.AVI
SEDUCING-A.AVI
SEDUCING-B.AVI
STAR-A.AVI
STAR-B.AVI
SURPRISING-A.AVI
SURPRISING-B.AVI
Scaring.AVI
SharingIcecream.AVI
Swimming.AVI
TENNIS-A.AVI
TENNIS-B.AVI

--
David V. Smith, Ph.D.
Assistant Professor of Psychology
Temple University
Weiss Hall, Room 825
1701 North 13th Street
Philadelphia, PA 19122
Office Phone: 215-204-1552
Lab Website: https://sites.temple.edu/neuroeconlab/

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] BedpostX for 7T Diffusion data

[Elam, Jennifer]

Hi Kamal,

No, we have not released bedpostX processed 7T diffusion data on HCP Young 
Adult subjects due to competing priorities, such as the advent of the Lifespan 
HCP-Development and HCP-Aging projects.


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 Shadi, Kamal 

Sent: Thursday, April 25, 2019 6:49:11 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] BedpostX for 7T Diffusion data


Dear HCP experts,



Is bedpostx data available for 7T dMRI scans?



Regards,

Kamal

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Eye tracking data for 3T scans?

[Elam, Jennifer]

Hi Nicola,

Yes, you are correct, we did not collect and release eye tracker data for 3T 
for HCP-Young Adult.


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 Nicola Toschi 

Sent: Friday, April 19, 2019 4:03:20 AM
To: hcp-users@humanconnectome.org >> hcp-users
Subject: [HCP-Users] Eye tracking data for 3T scans?

Dear List,

from what I understand from the S1200 Manual, eye tracking data is not
available for 3T fMRI rest data (only for 7T data)? Is this correct?

I just wanted to double check as this relates to a referee request for a
submitted paper.

Thank you very much in advance,

Nicola

--
_
Prof. Nicola Toschi

Associate Professor of Medical Physics
Medical Physics Section - Department of Biomedicine and Prevention
University of Rome "Tor Vergata"
Via Montpellier 1 - 00133 Rome (IT)
tos...@med.uniroma2.it

Research Staff, Associate Investigator
A.A. Martinos Center for Biomedical Imaging - Harvard Medical School/MGH
149 13th street, 02129 Boston (MA), USA
nic...@nmr.mgh.harvard.edu


---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Become an HCP Pipelines pro at HCP Course 2019!

[Elam, Jennifer]

Want to apply tools created by HCP experts to your own neuroimaging data?
Always wanted to try the HCP Pipelines, but haven't had the time to test them 
out?

This year's HCP Course July 8 – 12, 2019 in Portland, Oregon is featuring 
expanded, hands-on sessions to help you discover and use HCP neuroimaging 
analysis pipelines. Course attendees will even have the opportunity to try the 
HCP Pipelines out on their own data!

HCP Pipelines demystified. Hands-on practice. Your data, processed.
We'll cover...

  *
Best practices for high quality image acquisition
  *
Strengths of the HCP's neuroanatomically-driven approach to preprocessing and 
registration
  *
Unique features of the HCP Pipelines within the growing constellation of 
open-source neuroimaging analysis tools
  *
Organizing your imaging data to run the pipelines
  *
Diving into the scripts to see what is happening at each step of the processing
  *
Editing the pipeline code and parameters to fit your specific needs
  *
Running the pipelines in a ready to use container and turnkey framework locally 
or on the cloud to get results
  *
Interfacing pipelines in container turnkey form with the XNAT informatics 
ecosystem
  *
Tips on how to handle legacy data

Plus, understanding HCP processing will put you in a great position to utilize 
the soon-to-be-released HCP Lifespan Development (ages 5-21) and Aging (ages 
35-100+) data and upcoming Connectomes Related to Human Disease projects.
For more info visit the 

 HCP Course 2019 
website.
 Register soon, the course is filling up fast!

If you have any questions, please contact us at: 
hcpcourse@humanconnectome.org

We look forward to seeing you in Portland!
Best,
2019 HCP Course Organizers

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] TR : tutorial: resting state fMRI Scene is not working well with Connectome Workbench 1.3.2

[Elam, Jennifer]

Hi Vanessa,

Sorry that the Charting Dense Timeseries section of the Scene 4 section of the 
Workbench Tutorial is not working. There was a major update to charting 
features in wb_view with the release of WB v1.3.0+. Due to other priorities we 
have not updated the WB Tutorial to incorporate those changes.


However, you can get around the problem using the "Chart Old" view by replacing 
the first 3 steps:


• Select FileNew Tab (shortcut Cmd/Ctrl + T). A new Viewing Tab will be 
created (3) Montage. Click Yes on the warning.

• Select ViewTile Tabs ConfigurationEdit Tile Tabs Configurations...  to and 
swtich to Custom with dimensions Rows 2 and Columns 2 to show the new tab in 
Tile Tabs.

• Change the View in the Toolbar to Chart Old. The Charting tab is 
automatically activated in the Overlay Toolbox.

• Click the Select checkbox in the Overlay Toolbox:Charting:Loading tab to turn 
on charting of the loaded CP10101 dense time series (*dtseries) file when 
brainordinates are selected.


proceed with the rest of the instructions in that section


We can also answer questions on charting here on the list if you are interested 
in using this feature for your own work.


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 DE CASTRO Vanessa 

Sent: Tuesday, April 2, 2019 8:26 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] TR : tutorial: resting state fMRI Scene is not working 
well with Connectome Workbench 1.3.2

Sorry, the tittle of the object from the previous message is not correct :/ 
I mean that is not working well with Connectome Workbench 1.3.2

--

Vanessa DeCastro, PhD

Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
Pavillon Baudot CHU Purpan
31052 Toulouse Cedex 03, France


De : DE CASTRO Vanessa
Envoyé : mardi 2 avril 2019 14:48
À : hcp-users@humanconnectome.org
Objet : tutorial: resting state fMRI Scene is not working well with SPM 12

Tutorial v.1.0.pdf. Page 23: Charting dense timeseries

1- New tab: Is not the CortexLeft, just Montage

2- When I change the View to Charge, I must disable Tile Tabs to see the graph, 
but I really don't know to what correspond

3- Click the Select checkbox in the Overlay Toolbox:Charting:Loading = I can't 
click because is disable the tab. So then, I can't go further to next steps 
through this Scene.


Yours Sincerely
--

Vanessa DeCastro, PhD

Centre de Recherche Cerveau et Cognition - UMR 5549 - CNRS
Pavillon Baudot CHU Purpan
31052 Toulouse Cedex 03, France


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Connectome workbench download security certificate

[Elam, Jennifer]

Hi Tom,

The certificates were updated yesterday, clearing your browser cache should 
solve the problem. Let us know, if not.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Elam, Jennifer 

Sent: Wednesday, March 27, 2019 11:05:04 AM
To: Veale, Thomas; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Connectome workbench download security certificate


Thanks Tom, we'll look into it and let you know when things are back up.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Veale, Thomas 

Sent: Wednesday, March 27, 2019 10:57:59 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Connectome workbench download security certificate


Dear HCP,



Just to let you know the download links for the connectome workbench 
(https://www.humanconnectome.org/software/get-connectome-workbench#download) 
appear to be unsecure (certificate has expired). Meaning I’m unable to access 
the downloads. This seems to be the case for all platform download links.



Any help in resolving this would be much appreciated.



Many Thanks,

Tom





Tom Veale

PhD Student

Address: Dementia Research Centre,

UCL Queen Square Institute of Neurology,

First Floor, Russell Square House,

University College London

Telephone: 02031 086222



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Connectome workbench download security certificate

[Elam, Jennifer]

Thanks Tom, we'll look into it and let you know when things are back up.


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 Veale, Thomas 

Sent: Wednesday, March 27, 2019 10:57:59 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Connectome workbench download security certificate


Dear HCP,



Just to let you know the download links for the connectome workbench 
(https://www.humanconnectome.org/software/get-connectome-workbench#download) 
appear to be unsecure (certificate has expired). Meaning I’m unable to access 
the downloads. This seems to be the case for all platform download links.



Any help in resolving this would be much appreciated.



Many Thanks,

Tom





Tom Veale

PhD Student

Address: Dementia Research Centre,

UCL Queen Square Institute of Neurology,

First Floor, Russell Square House,

University College London

Telephone: 02031 086222



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] HCP pipelines v4.0.0 released!

[Elam, Jennifer]

Apologies for the double posting, but there was a glitch with the end of the 
pipelines announcement just sent:


We are very happy to announce the release of v4.0.0 of the HCP 
pipelines<https://github.com/Washington-University/HCPpipelines/releases>!!!


Notable changes and features of v4.0.0

  *   First supported release of multi-run FIX (MR-FIX)
  *   Added support for FreeSurfer 6 (with HCP-specific customizations) and 
support for manual editing
  *   Added FSL 6.0.1 compatibility
  *   Added polynomial detrending option to MR-FIX
  *   Added motion regression argument to FIX
  *   Improved Octave compatibility in FIX
  *   Consolidated all the FIX related scripts into the ‘ICAFIX’ folder
  *   Improved support for compiled MATLAB
  *   Extended scripts to accept ‘i/j/k’ for phase encoding directions 
(matching BIDS nomenclature)
  *   Added and improved various comments, READMEs, usage statements
  *   Numerous minor bugfixes and tool version checks

If you are interested in getting hands on experience with using the HCP 
Pipelines, we recommend joining us at the 2019 HCP Course July 8-12 in 
Portland, 
OR<https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php><https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php>.


This year's course will have expanded coverage of the pipelines for all levels 
of users. Meet and bring your questions to the HCP pipelines creators, gain 
practical experience that you can use on your data, and learn about the new 
data being released and processed with the updated pipelines.


Best,

WU-Minn-Oxford HCP Consortium


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Elam, Jennifer 

Sent: Monday, March 18, 2019 10:23:25 AM
To: hcp-users@humanconnectome.org >> hcp-users; hcp-annou...@humanconnectome.org
Subject: [HCP-Users] HCP pipelines v4.0.0 released!

We are very happy to announce the release of v4.0.0 of the HCP 
pipelines<https://github.com/Washington-University/HCPpipelines/releases><https://github.com/Washington-University/HCPpipelines>!!!


Notable changes and features of v4.0.0

  *   First supported release of multi-run FIX (MR-FIX)
  *   Added support for FreeSurfer 6 (with HCP-specific customizations) and 
support for manual editing
  *   Added FSL 6.0.1 compatibility
  *   Added polynomial detrending option to MR-FIX
  *   Added motion regression argument to FIX
  *   Improved Octave compatibility in FIX
  *   Consolidated all the FIX related scripts into the ‘ICAFIX’ folder
  *   Improved support for compiled MATLAB
  *   Extended scripts to accept ‘i/j/k’ for phase encoding directions 
(matching BIDS nomenclature)
  *   Added and improved various comments, READMEs, usage statements
  *   Numerous minor bugfixes and tool version checks

If you are interested in getting hands on experience with using the HCP 
Pipelines, we recommend joining us at the 
<https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php>
 
<https://store.humanconnectome.org/courses/2019/exploring-the-human-connectome.php>
 .


This year's course will have expanded coverage of the pipelines for all levels 
of users. Meet and bring your questions to the HCP pipelines creators, gain 
practical experience that you can use on your data, and learn about the new 
data being released and processed with the updated pipelines.


Best,

WU-Minn-Oxford HCP Consortium


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP pipelines v4.0.0 released!

[Elam, Jennifer]

We are very happy to announce the release of v4.0.0 of the HCP 
pipelines!!!


Notable changes and features of v4.0.0

  *   First supported release of multi-run FIX (MR-FIX)
  *   Added support for FreeSurfer 6 (with HCP-specific customizations) and 
support for manual editing
  *   Added FSL 6.0.1 compatibility
  *   Added polynomial detrending option to MR-FIX
  *   Added motion regression argument to FIX
  *   Improved Octave compatibility in FIX
  *   Consolidated all the FIX related scripts into the ‘ICAFIX’ folder
  *   Improved support for compiled MATLAB
  *   Extended scripts to accept ‘i/j/k’ for phase encoding directions 
(matching BIDS nomenclature)
  *   Added and improved various comments, READMEs, usage statements
  *   Numerous minor bugfixes and tool version checks

If you are interested in getting hands on experience with using the HCP 
Pipelines, we recommend joining us at the 

 

 .


This year's course will have expanded coverage of the pipelines for all levels 
of users. Meet and bring your questions to the HCP pipelines creators, gain 
practical experience that you can use on your data, and learn about the new 
data being released and processed with the updated pipelines.


Best,

WU-Minn-Oxford HCP Consortium


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP Course 2019: Get ready for more data, and a new way of getting it

[Elam, Jennifer]

More HCP data are comingand will be released in a new way.will you be 
ready?

This spring, the first data from the Lifespan Human Connectome Projects - (HCP) 
Development (healthy subjects ages 5-21) and HCP Aging (ages 36-100+) will be 
publicly released. Yay!

Also, for the first time, we will be releasing these data on the cloud, via the 
NIMH Data Archive (NDA). This will enable computing on the cloud to analyze HCP 
and Lifespan data.

Come to the 2019 HCP Course: "Exploring the Human 
Connectome",
 July 8 – 12, 2019 in Portland, Oregon, USA to learn all about the new data, 
how to access it on NDA, and using HCP methods, tools, and pipelines on your 
own neuroimaging data.
This 5-day intensive course will provide training in acquisition, processing, 
analysis and visualization of whole brain imaging and behavioral data of humans 
and non-human primates using methods and tools developed by the WU-Minn-Oxford 
HCP consortium. Both new and current users of HCP data, methods, and tools are 
welcome and the course will cover both basic and advanced topics.

For more info and to register visit the HCP Course 2019 
website.
 If you have any questions, please contact us at: 
hcpcou...@humanconnectome.org
We look forward to seeing you in Portland!

Best,
2019 HCP Course Organizers

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] A few questions about HCP behavioral data

[Elam, Jennifer]

Hi Xinyang, Mattis, and Kristina,

Item Response Theory (IRT) was used to score the HCP Toolbox data, but this was 
done completely internally by the NIH Toolbox processing team and we don't have 
any other details beyond what is described in the NIH Toolbox Scoring and 
Interpretation Guide from August 2012 that we provided you. From what that 
Guide says, I believe the IRT statistical model was constructed from the NIH 
Toolbox norming sample, but we do not know the details about the type of IRT 
model.

You can ask the NIH Toolbox helpdesk for more clarification by writing them. We 
correspond with Odessa Castro at Toolbox through the 
h...@nihtoolbox.org email address.


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 Xinyang Liu 

Sent: Thursday, February 21, 2019 7:19:24 AM
To: HCP 讨论组
Subject: [HCP-Users] A few questions about HCP behavioral data

Dear HCP experts,

We're currently analyzing some of the behavioral data from your dataset and 
have three short questions about the IRT-modelling and theta-score derivation 
that is also mentioned in the "NIH Toolbox Scoring and Interpretation Guide". 
To be able to build comparable scores between NIH-task data and Penn- and 
Working Memory data we would like to know more about the NIH IRT-scores. We 
hope you can help us out.

  1.  In the "NIH Toolbox Scoring and Interpretation Guide" it is mentioned 
that IRT-scores were calculated before the consecutive scores, such as 
Age-adjusted or Unadjusted. Was that also true for the HCP data?
  2.  What was the database to estimate the IRT model for the HCP data? Was the 
model estimated based on the HCP data only or was it somehow combined with the 
norming sample of the NIH Toolbox?
  3.  What type of IRT model was run? A simple Rasch model or did you add other 
free parameters, such as guessing probability (2PL)?

Thank you very much for your help.

Kind regards,
Xinyang







___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric measures

[Elam, Jennifer]

Hi Caio,

Ideally you would share the data both ways, as your original arbitrary files 
and converted and visually displayed as parcel x parcel pconn CIFTI files on 
the cortex and/or in matrices in Workbench scene files. Alternatively (or 
additionally), you could just create scenes of your figure images from your 
paper, by loading image files into Workbench and display them -- I can give you 
further instructions on how to do this.


Either way you would then have a scene file that you can upload to BALSA along 
with your arbitrary files. BALSA could then display one of your scenes and have 
your study dataset be searchable on the BALSA homepage.


If you have any questions on how to put together your dataset for BALSA, please 
let me know.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: John Smith 
Sent: Friday, February 8, 2019 10:29:45 AM
To: NEUROSCIENCE tim
Cc: Caio Seguin; Elam, Jennifer; hcp-users
Subject: Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric 
measures

The "Upload Files" button on the Files modal should take you to a page with a 
widget that allows you to upload arbitrary files to your BALSA study. It is 
assumed that extra files are there to serve as documentation or additional 
figures, so currently the uploader accepts files with the following extensions: 
zip, txt, rtf, pdf, odt, odp, wpd, doc, docx, ppt, pptx, jpg, png, fig, m, gif, 
csv. A file of any type can be uploaded so long as it is in a directory 
contained in a zip file. Within that base directory, such files can be nested 
into other directories, and that is where they will appear when the dataset as 
a whole is downloaded. Any files uploaded outside of a zip will be assumed to 
exist at the base directory for the study. As a final note, files that are not 
directly used by a scene will not be downloaded unless the user has selected to 
download the entire study or has specifically selected those files for download.

-John

On Thu, Feb 7, 2019 at 5:08 PM Timothy Coalson 
mailto:tsc...@mst.edu>> wrote:
As I recall, BALSA also allows arbitrary additional files to be uploaded to 
studies.  I'm not sure about the details of how to do this, though (there is an 
"upload files" button in the "files" modal for a study you own, but I'm not 
sure where those files end up).

Tim


On Thu, Feb 7, 2019 at 4:52 PM Caio Seguin 
mailto:caioseg...@gmail.com>> wrote:
Thanks Tim and Matt for the quick reply.

Most of the files are NxN connectivity matrices, where N could denote, for 
instance, ROIs from different parcellation schemes or resting-state functional 
networks.

Ok, so one option is to transform these matrices into cifti files and share 
them through BALSA. On the one hand, this is a nice solution for it solves the 
user term uses. On the other, it is a bit of a roundabout way to store these 
files in the context of my manuscript. The matrices are used to derive 
graph-theoretic measures about brain organization (rather than for 
visualization purposes), so researchers interested in that would need to 
convert the cifti files back to CSV.

More generally, do you suggest any methods to share HCP-derived files in an 
arbitrary format?

Thanks in advance for the help.

Best,
Caio


Em sex, 8 de fev de 2019 às 06:19, Timothy Coalson 
mailto:tsc...@mst.edu>> escreveu:
If your data is organized as a value per parcel/network, you should be able to 
turn it into parcellated cifti files, which can be displayed in wb_view (and 
therefore in scenes) as a matrix and/or as colored regions on the surfaces and 
in the volume.

See wb_command -cifti-parcellate (to make a template parcellated cifti file you 
can use to import data into), -cifti-label-import (to get your network ROIs 
into the format -cifti-parcellate wants), and -cifti-convert (and its 
-from-text option, to read csv or other text data and output cifti).

Tim


On Thu, Feb 7, 2019 at 7:05 AM Caio Seguin 
mailto:caioseg...@gmail.com>> wrote:
Dear experts,

I have used diffusion and resting-state functional MRI data from the HCP to 
derive whole brain connectomes for individual participants. I used the 
connectomes to computed graph-theoretic measures that are part of a manuscript 
I am working on.

My question concerns the sharing of these connectomes and graph-theoretic 
measures. My current understanding is that sharing this data is ok as long as I 
make sure users abide to the HCP data usage terms. What are your suggestions on 
how to do this?

I've seen BALSA proposed to this end, since it provides a built-in mechanism of 
user terms, but my files are CSV or .mat files rather than WB sc

Re: [HCP-Users] Request for DTIV1_to_Workbench.sh

[Elam, Jennifer]

Hi Sally,

Thanks for pointing us to the earlier message to the list with the script. I'll 
forward it to you with the attachments off the list and add it to our wiki for 
others to get if they need it.


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 Durgerian, Sally 

Sent: Wednesday, February 6, 2019 7:01:06 PM
To: hcp-users@humanconnectome.org
Cc: sallysgmail
Subject: [HCP-Users] Request for DTIV1_to_Workbench.sh


Dear Experts,

I'm interested in using the script DTIV1_to_Workbench.sh as described in the 
HCP course materials, but I don't want to have to download the entire course VM 
to get it. Is there a way of making that script available on GitHub or on the 
HCP web site? Note that it also requires Whole_Brain_Trajectory_1.25.nii.gz 
which I haven't been able to find outside the VM either.

I saw a thread in the past (Tue, 01 Mar 
2016)
 requesting this script, but when I clicked that link my browser removed the 
attachment saying it was a security hazard.

Thanks for your help.

Sally

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Inter-scan intervall of retst dataset

[Elam, Jennifer]

Hi Marlene,

See 
https://wiki.humanconnectome.org/display/PublicData/Interval+between+Test+and+Retest+Visits+for+HCP+Retest+Subjects

Interval between Test and Retest Visits for HCP Retest Subjects - Connectome 
Data Public - HCP Wiki - Human Connectome 
Project
wiki.humanconnectome.org
A subset of HCP twin pair Subjects were recruited for a full retest of the HCP 
3T scan protocol and behavioral battery in a second retest visit.

We can't give exact dates of test and retest because that would be subject 
identifying, but the data on the wiki does give number of months between test 
and retest.

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 Marlene Tahedl 

Sent: Friday, January 25, 2019 10:34:27 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Inter-scan intervall of retst dataset

Hi all,

I'd be interested to know the exact inter-scan intervall of the retest HCP 
dataset: I cannot find any exact dates in the manual, it only says that the 
subjects came back on "another" day - how long was that second scan after the 
first?

Thanks and cheers,
Marlene.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Detailed manual rating score of structural images

[Elam, Jennifer]

Hi Xuhong,

All of the structural data released by HCP is of good or excellent quality 
(scores of 3-4 on our QC scale). We have not publicly released the exact 
ratings for released subjects. The file you are referring to is on our 
non-public wiki and is referred to as an example in the SOP for other groups 
who are setting up neuroimaging projects to understand how we did things for 
HCP.


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 Xuhong Liao 

Sent: Tuesday, January 22, 2019 3:57:09 AM
To: hcp-users; Harms, Michael
Subject: Re: [HCP-Users] Detailed manual rating score of structural images

Many thanks,

I noticed that the standard QC rating (1 = Poor, to 4 = Excellent) of each 
T1/T2 weighted image was added in the 'Phasell_T1W/T2w_QC.xls' located on the 
HCP wiki (https://wiki.humanconnectome.org/dashboard.action). But this link is 
fail to open. How can I obtain these rating scores?

Regards,
Xuhong Liao

Xuhong Liao, Ph. D, Associate Professor
School of Systems Science,
Beijing Normal University
No.19 Xinjiekouwai Street,
Beijing, 100875, China
liaoxuh...@gmail.com



mailto:hcp-users-requ...@humanconnectome.org>>
 于2019年1月21日周一 上午2:00写道：
Send HCP-Users mailing list submissions to
hcp-users@humanconnectome.org

To subscribe or unsubscribe via the World Wide Web, visit
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
or, via email, send a message with subject or body 'help' to

hcp-users-requ...@humanconnectome.org

You can reach the person managing the list at

hcp-users-ow...@humanconnectome.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of HCP-Users digest..."
Today's Topics:

   1. Detailed manual rating score of structural images (Xuhong Liao)
   2. Re: Detailed manual rating score of structural images
  (Harms, Michael)



-- Forwarded message --
From: Xuhong Liao mailto:liaoxuh...@gmail.com>>
To: hcp-users 
mailto:hcp-users@humanconnectome.org>>
Cc:
Bcc:
Date: Sun, 20 Jan 2019 17:29:05 +0800
Subject: [HCP-Users] Detailed manual rating score of structural images
I have got the S-1200 dataset in which the subjects with QC issues are marked 
with codes from "A" to "E".

Could anyone tell me how to obtain the detailed manual rating scores of each 
subject described in the quality control SOP?

Regards,
Xuhong Liao, PhD
--
Xuhong Liao, Associate Professor
School of Systems Science,
Beijing Normal University
No.19 Xinjiekouwai Street,
Beijing, 100875, China
liaoxuh...@gmail.com




-- Forwarded message --
From: "Harms, Michael" mailto:mha...@wustl.edu>>
To: Xuhong Liao mailto:liaoxuh...@gmail.com>>, hcp-users 
mailto:hcp-users@humanconnectome.org>>
Cc:
Bcc:
Date: Sun, 20 Jan 2019 14:19:53 +
Subject: Re: [HCP-Users] Detailed manual rating score of structural images



Hi,



https://wiki.humanconnectome.org/pages/viewpage.action?pageId=88901591





--

Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: 
mha...@wustl.edu



From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xuhong Liao mailto:liaoxuh...@gmail.com>>
Date: Sunday, January 20, 2019 at 3:29 AM
To: hcp-users 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Detailed manual rating score of structural images



I have got the S-1200 dataset in which the subjects with QC issues are marked 
with codes from "A" to "E".



Could anyone tell me how to obtain the detailed manual rating scores of each 
subject described in the quality control SOP?



Regards,

Xuhong Liao, PhD

--

Xuhong Liao, Associate Professor

School of Systems Science,

Beijing Normal University

No.19 Xinjiekouwai Street,

Beijing, 100875, China

liaoxuh...@gmail.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended 

Re: [HCP-Users] SNP documentation

[Elam, Jennifer]

Hopefully someone else on the list with more experience using genetic data can 
comment. We don't have any official documentation on using the HCP dbGaP data 
other than that available along with the dataset in dbGaP itself.


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 Max Bertolero 

Sent: Thursday, January 17, 2019 11:05:07 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] SNP documentation

Does anyone have documentation that they can share on how to find SNPs for each 
gene / subject in the dbGaP data?

Max Bertolero, PhD
maxbertolero.org


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Information of HCP Data

[Elam, Jennifer]

Hi Daniel,

You also will find some additional information on the tasks in the 3T Task fMRI 
scripts and protocol details section (p. 45) of the S1200 Release Reference 
Manual.


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 Glasser, Matthew 

Sent: Wednesday, January 9, 2019 9:41:50 AM
To: Daniel KRISTANTO; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Information of HCP Data

If you want to learn more about the tasks, there is a paper about them: 
https://www.sciencedirect.com/science/article/pii/S1053811913005272

What specifically are you wanting to do with the task data?  Unless you are 
actually interested in statistical significance information, effect sizes are 
more biologically valid.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Daniel KRISTANTO 
<18481...@life.hkbu.edu.hk>
Date: Wednesday, January 9, 2019 at 7:16 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Information of HCP Data

Dear Sir/Madam,

I am Daniel Kristanto, a PhD student at Hong Kong Baptist University. 
Currently, I am doing research with a topic of machine learning in neuroimaging 
and planning to use data from the HCP project. The data are currently available 
in our research group. However, I have some questions about the data, 
specifically in the within-subject analysis for task fMRI.
1. The first question is about the analyses done in each task. For instance, in 
the emotion task 
(MNINonLinear/Results/tfMRI_EMOTION/tfMRI_EMOTION_hp200_s4_level2.feat/Grayordin
 atesStats/cope1.feat), there are some files,
cope1.dtseries.nii
logfile mask.dtseries.nii
mean_random_effects_var1.dtseries.nii
pe1.dtseries.nii res4d.dtseries.nii
tdof_t1.dtseries.nii
tstat1.dtseries.nii
varcope1.dtseries.nii
weights1.dtseries.nii
zflame1lowerstat1.dtseries.nii
zflame1upperstat1.dtseries.nii
zstat1.dtseries.nii
My question is, where can I find detailed information about each 
file/analysis? For instance, if I am not mistaken, 'tstat1.dtseries.nii' means 
t-test.

2. The second question is about the contrast in each task. For example in 
Language task, there are 6 contrasts, which are MATH, STORY, MATH-STORY, 
STORY-MATH, neg_MATH, neg_STORY. Where can I find detailed information about 
each contrast? For instance, if I am not mistaken, MATH-STORY means the 
analysis on MATH task with STORY task as a baseline.

Those are my questions. I do really appreciate your attention and look forward 
to your answers.
Thank you.


Best regards,
Daniel Kristanto
PhD Student
Department of Physics
Hong Kong Baptist University
Hong Kong





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Wb-command Problem

[Elam, Jennifer]

Hi Ben,

You are not intended to double click wb_command or wb_import as applications, 
they are utilities that are used from a terminal or script (generally, after 
adding their location to your $PATH, per the install instructions in 
README.txt).  Double clicking them from a folder window is expected to make a 
window that closes immediately.


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 Benjamin Bao 

Sent: Thursday, December 27, 2018 9:41:06 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Wb-command Problem

Hello,
I have recently downloaded the workbench program on my windons 10 system. 
When I was trying to set a minimus cluster size, I have read that I need to use 
the wb_command program. However, immediate after I tried to open the program, 
it shuts off. I am wondering how should I proceed?
   I would really appreciate your help!

Sincerely
Ben Bao

Nipissing University


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Certification of Agreement to WU-Minn Human Connectome Project (HCP) Consortium Open Access Data Use Terms

[Elam, Jennifer]

Hi Michel,

The Open Access Data Use terms are here: 
https://www.humanconnectome.org/study/hcp-young-adult/document/wu-minn-hcp-consortium-open-access-data-use-terms

and can also be downloaded as a PDF from that site.


Do you need a letter certifying that you have signed the OADUT? If so, we can 
provide that too.

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 Michel Thiebaut 

Sent: Wednesday, December 12, 2018 8:54:03 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Certification of Agreement to WU-Minn Human Connectome 
Project (HCP) Consortium Open Access Data Use Terms

Dear experts,

Today I tried to access a document on the website Certifying the Agreement to 
WU-Minn Human Connectome Project (HCP) Consortium Open Access Data Use Terms 
but I'm afraid the link is broken
https://store.humanconnectome.org/?dataMessage=Content_Unavailable=/data/data-use-terms//

I was wondering whether you would have the kindness to provide me with the 
document or eventually repair the link. This is indeed for local admin purposes.

thank you so much.
mich

Michel Thiebaut de Schotten
Director of Research, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Installing HPC

[Elam, Jennifer]

Hi Ilaria,

Sign up for a ConnectomeDB account here: https://db.humanconnectome.org


Follow the instructions on pp. 24-25 of the S1200 Release Reference 
Manual
 to verify your account and sign the data use terms.


Once you have done that you should be able to download the tutorial data from 
the link on the Get Connectome Workbench page or on the S1200 project 
page within ConnectomeDB.


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 Ilaria Cinelli 

Sent: Tuesday, November 20, 2018 2:33:28 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Installing HPC

To whom it may concern,

I have downloaded the software but I cannot download the data for the tutorial.
Can you please help me?



Kind Regards,
Eng. Ilaria CINELLI PhD 
AFAsMA




Postdoctoral Scholar
Civil and Environmental Engineering
Tufts University
Anderson Hall 308F - 200 College Avenue
Medford
02155, MA

Phone(s): +39 3492182632; +17818271925
Email(s): i_cine...@yahoo.it ; ilaria.cine...@community.isunet.edu
Skype: tgcine



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Restricted access

[Elam, Jennifer]

Hi Jodi,

Let me have the database people look into this.


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 Gilman, Jodi 

Sent: Tuesday, October 9, 2018 1:05:11 PM
To: hcp-users@humanconnectome.org
Cc: Potter, Kevin
Subject: [HCP-Users] Restricted access

Hello,

I applied for (and was granted) access to the restricted HCP database; however, 
when I log onto https://db.humanconnectome.org/data/projects/HCP_1200
I no longer see an option to download the restricted data. Please help!

Best,
Jodi

Jodi Gilman, Ph.D.
Associate Professor, Harvard Medical School
Center for Addiction Medicine
Massachusetts General Hospital
101 Merrimac St.
Boston, MA 02114
Tel.:617-643-7293
Fax:617-643-1998


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] 2018 HCP Course Materials including Virtual Machine now available!

[Elam, Jennifer]

Announcing the release of all 2018 HCP Course materials, including lectures, 
practicals, and the course computer virtual machine (VM) with all software and 
data for completing practicals. These materials are available download from the 
2018 HCP Course 
site.
 The course VM download requires VMware software and at least 1TB of hard drive 
space.

Please let us know if you have any questions or have problems with the VM 
download.

Thanks!
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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] s3://hcp-openaccess-temp bucket retired

[Elam, Jennifer]

Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket:
Now that access to HCP Open Access data via the AWS s3://hcp-openaccess/ bucket 
has been restored, as of today, we have retired the temporary 
s3://hcp-openaccess-temp/ bucket.

Please use the s3://hcp-openaccess/ bucket to access HCP AWS Public Dataset 
data. If you have been accessing data via the temp bucket, your current access 
keys should still be usable for accessing data in the hcp-openaccess bucket. 
However, if you run into any permissions issues, try regenerating your access 
keys.

Best,
HCP Staff

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Individual Functional Connectivity Matrix

[Elam, Jennifer]

Hi Bryan,

See HCP-Users FAQ 
#3
 for instructions on computing functional connectivity for individual subjects 
using Connectome 
Workbench 
wb_command.


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 Zhuochen Wang 

Sent: Wednesday, September 26, 2018 2:40:07 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Individual Functional Connectivity Matrix


Hi,


I noticed in the user manual that only group-level matrix was computed in the 
dataset. However, I would like to compute the functional connectivity matrix 
for individual HCP rsfMRI data. I was wondering if there might be any pipeline 
available to achieve that on MELODIC processed HCP rsfMRI data? Thank you!


Best,

Bryan (Zhuochen) Wang, M.S.
Project Assistant

USC Stevens Neuroimaging and Informatics Institute
Laboratory of Neuro Imaging (LONI)
Keck School of Medicine of USC
University of Southern California 

2025 Zonal Ave.
Los Angeles, CA 90033


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Intermediate freesurfer files not available through CREST?

[Elam, Jennifer]

This wiki page might help: 
https://wiki.humanconnectome.org/display/PublicData/How+To+Access+Subject+Data+via+REST

How To Access Subject Data via REST - Connectome Data 
...
wiki.humanconnectome.org
For the HCP 1200 Release, unprocessed and processed data for a subject can be 
accessed via REST calls apart from using other modes such as Connectome In a 
Box, Aspera, Amazon AWS.. In order to access data for a subject, you will need 
to register at https://db.humanconnectome.org To get data via REST, in a 
script, you could use tools like curl. Data organization

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 Harms, Michael 

Sent: Tuesday, September 25, 2018 10:22:40 AM
To: Nicola Toschi; hcp-users@humanconnectome.org >> hcp-users
Subject: Re: [HCP-Users] Intermediate freesurfer files not available through 
CREST?


They should be.

Have you searched the list for previous recipes for REST calls into the CREST 
resource?  It may be simply that your path isn't correct.
The FS data folder structure begins at /T1w/, so you probably 
want something like /T1w//surf/lh.white


--
Michael Harms, Ph.D.

---

Associate Professor of Psychiatry

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave.Tel: 314-747-6173

St. Louis, MO  63110  Email: mha...@wustl.edu

On 9/25/18, 9:56 AM, "Nicola Toschi"  wrote:

Hi Michael,

thank you for your reply.

I am working with the whole S1200 release would actually much prefer to
fetch only the files I need (namely surfaces, thickness, area, curvature
and jacobian - more or less) in a targeted way (not least because of
data footprint issue on compute clusters).

Are those files available via CREST?

Thank you!

nicola


On 09/25/2018 03:17 PM, Harms, Michael wrote:
> Hi,
> You can obtain the entire FreeSurfer output via the Structural Extended 
> packages.  Perhaps that would be an easier way for you to proceed?
>
> Cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave.Tel: 314-747-6173
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
> On 9/24/18, 6:25 PM, "hcp-users-boun...@humanconnectome.org on behalf of 
> Nicola Toschi"  tos...@med.uniroma2.it> wrote:
>
> Hello List,
>
> I am trying to retrieve the files present in the 'surf' directory of the
> freesurfer reconstruction via CREST. However, when trying to retrieve
> (e.g) lh.white I always end up with a file containing only error messages.
>
> I would be grateful for any pointers. below is an example of my curl
> call after opening a session.
>
> curl --cookie JSESSIONID= -O
> https://db.humanconnectome.org/data/archive/projects/HCP_1200/subjects/100307/experiments/100307_CREST/resources/100307_CREST/files/T1w/surf/lh.white
>
> Thank you very much in advance!
>
> Nicola
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] seeking a dataset for research

[Elam, Jennifer]

Hi Givon,

HCP data is MRI and MEG-based neuroimaging data at the resolution of 
millimeters of brain volume and surfaces rather than at neuronal resolution. 
Perhaps others on the list are aware of datasets with the information you are 
seeking.


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 Givon 

Sent: Monday, September 17, 2018 5:03:53 PM
To: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] seeking a dataset for research

Hi,

I am seeking a dataset for research.  I came across your dataset in
Amazon's registry of Open Data.   I am a computer scientist and do my
own private research.  Several years ago, I donated my computer
expertise to Mt. Sinai's neurology dept.  From that episode, I had an
inspiration about the composition of brain waves and the operation of
the neural network of the brain.  I am looking for a dataset, that
includes the voltages of neurons prior and during firing based upon
image or stimuli recognition.  Does your data have anything like that?
Would you know of such a dataset?

Thanks.  Much appreciated.

Sincerely,

Givon


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP AWS s3://hcp-openaccess-temp/ bucket retires Oct 1

[Elam, Jennifer]

Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket:
Now that access to HCP Open Access data via the AWS s3://hcp-openaccess/ bucket 
has been restored, we will be retiring the temporary s3://hcp-openaccess-temp/ 
bucket as of Monday Oct 1, 2018.

Over the next couple of weeks, please discontinue use of 
s3://hcp-openaccess-temp/ and move back to s3://hcp-openaccess/ for your 
analyses.
You do not need to generate new AWS access keys to access the 
s3://hcp-openaccess/ bucket if your keys for accessing the temp bucket are 
currently valid.

Best,
HCP Staff

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP AWS data back in s3://hcp-openaccess/ bucket

[Elam, Jennifer]

Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket:
The migration of HCP data to a new AWS account is now complete and access to 
the AWS s3://hcp-openaccess/ bucket has been restored. You may still access HCP 
Open Access data via the temporary s3://hcp-openaccess-temp/ bucket that has 
been in use since we started migrating the data in July, but that bucket will 
eventually be retired. This change does not require generation of new AWS 
access keys. You can use the same keys to access both buckets.


Thank you for your patience during the transition and let us know if you have 
any questions.



Best,

HCP Staff

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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>




From: hcp-users-boun...@humanconnectome.org 
 on behalf of Elam, Jennifer 

Sent: Monday, July 2, 2018 3:12 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] HCP AWS data moving to temporary bucket location on July 
5th, 2018


Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket:

Recent changes in the AWS Public Dataset Program have required migration of HCP 
data stored in AWS S3 to a new account.  As part of this transition, we must 
temporarily disable access to the current s3://hcp-openaccess/ bucket and make 
the data available through a temporary bucket location 
(s3://hcp-openaccess-temp/).  It is expected that the migration may take 4 – 6 
weeks.  During this time, data will be available via the temporary bucket 
location.



Once the original bucket has been fully migrated to the new account, we will 
announce that the migration is complete and you will once again access the data 
via the original bucket (s3://hcp-openaccess).  We anticipate transition to the 
temporary bucket to occur this Thursday, July 5th, 2018.  This change will 
require you to regenerate your AWS credentials via ConnectomeDB.  Once this 
change occurs, you will see a message on the ConnectomeDB login page that 
notifies of the change and will also receive notification of the new, temporary 
bucket as you recreate your credentials (access keys).



There may be a short time; several hours to a day or so, where the original 
bucket still works with your existing access keys.  Soon thereafter, however, 
access to the s3://hcp-openaccess bucket will be removed so that the bucket can 
be transitioned to the new account.



Let us know if you have any questions and thank you for your patience during 
this transition.



Best,

HCP Staff


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] HCP Development - DTI protocol

[Elam, Jennifer]

Hi Reut,

HCP Development uses a protocol based on the CCF Protocol template, which is 
available as a zip download of electronic protocols for import into a Siemens 
3T Prisma for all MR modalities used, including dMRI: 
http://protocols.humanconnectome.org/CCF/


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 Reut Moran 

Sent: Thursday, September 6, 2018 6:55:12 AM
To: HCP-Users@humanconnectome.org
Subject: [HCP-Users] HCP Development - DTI protocol


My name is Reut and I'm starting my PhD in Tel Aviv university in collaboration 
with Sheba medical center in Israel, on the subject of pediatric brain injury.
We are planning to begin scanning children in this study within the next few 
weeks. We are interested to run a very similar imaging protocol as is ran in 
the HCP Development Project, using a PRISMA scanner.
We followed the imaging acquisition on your website, however we did not find 
the DTI protocol.  Is it possible to refer me to where I can find this 
information?
Thank you in advance

Reut Moran

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] completely processed HCP data

[Elam, Jennifer]

Here's the documentation for the PTN release: 
https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP1200-DenseConnectome+PTN+Appendix-July2017.pdf


The PTN datasets are available for download at 
https://db.humanconnectome.org/data/projects/HCP_1200 (login and acceptance of 
HCP Open access terms required).


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 Glasser, Matthew 

Sent: Wednesday, September 5, 2018 3:20:05 AM
To: Bo Xu; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] completely processed HCP data

Have a look at the PTN release.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Bo Xu mailto:box...@gmail.com>>
Date: Wednesday, September 5, 2018 at 12:50 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] completely processed HCP data

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



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Question regarding intracranial volume

[Elam, Jennifer]

Hi Dimitri,

The intracranial volume estimates we report are outputs from FreeSurfer which 
reports values in mm3. See http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV


Others may want to comment on your finding that the average ICV in males in the 
S900 was 1700 vs. 1500 in other studies.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: D. van der Linden 
Sent: Thursday, August 30, 2018 8:01:52 AM
To: Elam, Jennifer; Benjamin Risk
Cc: hcp-users@humanconnectome.org
Subject: Question regarding intracranial volume


Dear sir, madam,



I have a question regarding the HCP data.

In the data there are various measures of brain volume and also an estimate of 
intracranial volume.

It was not clear however whether those values represent voxels or mm3?



For example the average intracranial volume in the HCP 900 batch was around 
1700 for males, which seems higher than the values around 1500mm3 that are 
reported in several studies.



So, my question is:

Do the intracranial values represent mm3 or voxels, or something else?



Kind regards,



Dimitri van der Linden

Erasmus University Rotterdam

The netherlands



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Unable to download data even if test on IBM Aspera Connect was all OK

[Elam, Jennifer]

Hi Tong,

Our IT expert says:

His machine needs to connect asp-connect1.wustl.edu, not the other way around.


Hopefully that information will help you and your IT get you connected.

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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Wu, Tong 
Sent: Wednesday, August 29, 2018 7:56:38 AM
To: Elam, Jennifer; hcp-users@humanconnectome.org
Subject: RE: [HCP-Users] Unable to download data even if test on IBM Aspera 
Connect was all OK


Dear Jenn,



I’ve forward the email to IT in my institute. I also added TCP Port 33001 as a 
special connection in the Windows firewall (inbound, UDP 33001 was added 
before). IT told me that the two ports shall be able to access remote servers. 
However, I tried again, the downloading is still not working. I’ll need to 
download data at ~10 GB size, and ~10-30TB. I can try to download the smaller 
size data at home, but this won’t work for the massive data.



May I know if we shall guarantee: 1)  my machine’s TCP 33001 and UDP 33001 be 
able to access your Aspera server and 2) HCP Aspera server will be able to 
access the two ports of my machine too?  I’m not very sure if the two are 
different things.



Thank you very much!



Best,

Tong



From: Elam, Jennifer 
Sent: 24 August 2018 19:10
To: Wu, Tong ; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Unable to download data even if test on IBM Aspera 
Connect was all OK



Hi Tong,

Our Aspera server is configured to use TCP and UDP Port 33001 for file 
transfers instead of a common port such as Port 22. If you are downloading from 
behind an institutional firewall, please speak with your IT people to ensure 
that Port 33001 is open to both TCP and UDP traffic. You also might try 
downloading at home where you might not have as many firewalls set up.



Let us know if you still have 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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>





From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Wu, Tong mailto:tong...@ucl.ac.uk>>
Sent: Friday, August 24, 2018 11:08:56 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] Unable to download data even if test on IBM Aspera Connect 
was all OK



Dear HCP user team,



I’m trying to download data from ConnectomeDB using the Aspera plugin. However, 
even if online test tool from IBM Aspera says that my system status is all OK 
(OS, ROWSER, connect, TCP and UDP ports), I still cannot download data. For 
example, if I click the link to download  1003 Subjects, recon r177 + r227, PTN 
Release<https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=GroupAvg=HCP1200_Parcellation_Timeseries_Netmats.zip>
 (13GB), Aspera never manages to connect successfully, but gives 'Error: Error 
establishing HTTP connection (check HTTP port and firewall)'.



I have closed windows firewalls, uninstalled anti-virus softwares, and checked 
on IBM Aspera websites. Then used their online tool to test my system, but it 
give all OK reports as described above.



In AWS, I can only see files organised subject by subject, but not these 
organised data packages. So still want to use Aspera.



May I know if there are any solutions to this?



Thank you very much!



Best,

Tong



___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Workbench v1.3.2 Released

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
August 28, 2018

Connectome Workbench v1.3.2 Released
Announcing the release of version 1.3.2 of Connectome 
Workbench 
(WB) brain visualization and analysis software. This release fixes a few bugs 
and adds some features, most notably Annotation substitutions, which allows one 
to efficiently make a series of annotations (text labels) with content loaded 
from a CSV file (*.wb_annsub.csv).

The Workbench distribution, available for 64-bit Mac OSX, Windows, and Linux, 
includes wb_view, a GUI-based visualization platform, and wb_command, a 
command-line program for performing a variety of algorithmic tasks using 
volume, surface, and grayordinate data.

Changes in Workbench v1.3.2
wb_view:
New Features

  *   Yoked annotation substitutions (and updates in Workbench Help and Guide 
to 
Annotations)
  *   Updates to BALSA Upload dialog including notification of updated 
extraction directory prefix
  *   Tab number always included in the name of the tab since some GUI controls 
(volume surface outline) use the tab number

Bug Fixes

  *   Fixes for sizing of color bars
  *   Missing QT SVG library has been added to Linux distributions

wb_command:
New Features

  *   new -surface-geodesic-all-to-all command
  *   fwhm estimation now has "whole file" and "demean" options

Notes on launching Workbench: (1) wb_command must be run from a terminal window 
(not double-clicked on Mac or Windows); (2) wb_view may crash if used with a 
remote desktop due to problems with Xcb and OpenGL in the remote desktops.  
VirtualGL works for some users.  Even if wb_view runs in a remote desktop, 
performance may be poor as they often use software implementations of OpenGL.

WB v1.3.2 is compatible with the WB v1.0 tutorial and the processed 1200 
Subjects Group Average Data available to download at 
http://humanconnectome.org/connectome/get-connectome-workbench.html and on the 
ConnectomeDB HCP project 
page. Access to both 
datasets require ConnectomeDB login and signature of the HCP Open Access Data 
Use Terms.

To download the WB v1.3.2 source code from 
GitHub: follow the link, 
click Releases (near the top center of the page), then under v1.3.2, click the 
“Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to 
the hcp-users discussion list (sign up 
here).

Best,
The WU-Minn HCP Consortium


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Unable to download data even if test on IBM Aspera Connect was all OK

[Elam, Jennifer]

Hi Tong,

Our Aspera server is configured to use TCP and UDP Port 33001 for file 
transfers instead of a common port such as Port 22. If you are downloading from 
behind an institutional firewall, please speak with your IT people to ensure 
that Port 33001 is open to both TCP and UDP traffic. You also might try 
downloading at home where you might not have as many firewalls set up.


Let us know if you still have 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 Wu, Tong 

Sent: Friday, August 24, 2018 11:08:56 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Unable to download data even if test on IBM Aspera Connect 
was all OK


Dear HCP user team,



I’m trying to download data from ConnectomeDB using the Aspera plugin. However, 
even if online test tool from IBM Aspera says that my system status is all OK 
(OS, ROWSER, connect, TCP and UDP ports), I still cannot download data. For 
example, if I click the link to download  1003 Subjects, recon r177 + r227, PTN 
Release
 (13GB), Aspera never manages to connect successfully, but gives 'Error: Error 
establishing HTTP connection (check HTTP port and firewall)'.



I have closed windows firewalls, uninstalled anti-virus softwares, and checked 
on IBM Aspera websites. Then used their online tool to test my system, but it 
give all OK reports as described above.



In AWS, I can only see files organised subject by subject, but not these 
organised data packages. So still want to use Aspera.



May I know if there are any solutions to this?



Thank you very much!



Best,

Tong



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Documentation HCP genetic data

[Elam, Jennifer]

We have replied to Yann off list, but for the benefit of others on the list who 
are interested in the HCP genetic data:

If you have questions about the HCP dbGaP data, please send them to 
dbgap-h...@ncbi.nlm.nih.gov – it’s a 
central collection place from where the questions are forwarded to the 
appropriate curator.


With our focus on the neuroimaging and behavioral data we distribute, we no 
longer have a team of geneticists consulting for the HCP, so you will get your 
best info from the dbGaP folks who are experts in using the genetic data they 
distribute.

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 LE GUEN Yann 

Sent: Tuesday, August 14, 2018 2:52:42 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Documentation HCP genetic data

Dear HCP users,

I am looking for the documentation of the HCP data online (other than the few 
pdfs and .txt in the downloaded data) ?

In particular, I would like to know a few things:

1) In which version genome build coordinates (GRCh37 or GRCh38) are the HCP 
genetic data released?

2) Is there any correspondence files for the SNPs names on the MEGA and Neuro 
chips ?
For example, (lines below do not provide confidential information on the 
subjects) the .bim starts this way:
11:49554-G-A049554GA
1JHU_1.55325055326TC
1JHU_1.56018056019CT
1JHU_1.61461061462AT
1JHU_1.661610661620A
1JHU_1.841380841390A
1JHU_1.86330086331GA
1JHU_1.88337088338AG
1rs3767239150915160A
1JHU_1.91535091536GT

I would like to convert JHU_* and CHR:POS-A1-A2 in rs ids names more commonly 
used such as rs376723915.

3) Maybe, I haven't looked carefully for it yet.. But, do you know where is the 
documentation describing the content of the genetic files such as 
ganon*_CHR.csv, infoCHR.csv, ganong*_CHR.sas7dbat, infoCHR.sas7dbat, 
fin_hcp_dose_cCHR_chunk*,  hcp_impute2_chrCHRchunk*, etc .. ? and recommended 
protocol to read/convert them for further analysis? These are text files likely 
readable as dataframes and their content is partly described by their columns 
names. However, I am looking for a documentation that would already gather all 
information and an efficient way to convert them to plink or bgen format 
(smaller binary files).

Best regards, Yann





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Movie stimulus question

[Elam, Jennifer]

Hi Dan,

To add to Keith's info, more detailed info on the 7T movie clip timing and on 
the origins of the clips themselves are in the attached CSVs which are also 
available on the HCP wiki: https://wiki.humanconnectome.org/x/coD4Bg


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 Keith Jamison 

Sent: Wednesday, August 15, 2018 10:51:31 AM
To: Lloyd, Dan
Cc: HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] Movie stimulus question

The movie lengths are:

MOVIE1: 921 seconds
MOVIE2: 918 seconds
MOVIE3: 915 seconds
MOVIE4: 901 seconds

These are the entire movie scan stimulus, including "REST".  Each subject's 
nifti/cifti data, as well as the other resources associated with it (WordNet, 
Motion Energy) matches these lengths as well.

Perhaps you are looking at MOVIE1 instead?

-Keith


On Wed, Aug 15, 2018 at 11:11 AM, Lloyd, Dan 
mailto:dan.ll...@trincoll.edu>> wrote:

Hello,

Movie 4 is 921 seconds long (with the last clip ending at 901 s, followed by 20 
sec of "rest").  The 7T cifti image series has 901 images.  Should we assume 
that the scan begins at the same time as the movie, and thus the movie runs 20 
seconds past the end of the scan?  (For all the movies, we're aiming for the 
exact match of screen events and functional images, and appreciate any 
pointers.  In general, does the movie begin as the scan begins, or is there a 
fixed offset, and if so is it the same for all four movies? )

Thank you!

Dan Lloyd


Trinity College, Connecticut, USA  06106
860 297 2528




___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
7T_MOVIE1_CC1_v2 Video TimingAll times in seconds
movie.block,block start time,block end time,block duration,Block = clip within movie
0,0,19.9583,19.9583,0 = 20s REST block between clips
1.1,20,264.0417,244.0417,
0,264.0833,284.0417,19.9583,
1.2,284.0833,505.7083,221.625,
0,505.75,525.7083,19.9583,
1.3,525.75,713.75,188,
0,713.7917,733.75,19.9583,
1.4,733.7917,797.5417,63.75,
0,797.5833,817.5417,19.9583,
1.5,817.5833,900.9583,83.375,
0,901,920.9583,19.9583,

7T_MOVIE2_HO1_v2 Video Timing
0,0,19.9583,19.9583,
2.1,20,246.7083,226.7083,
0,246.75,266.7083,19.9583,
2.2,266.75,525.,258.5833,
0,525.375,545.,19.9583,
2.3,545.375,794.5833,249.2083,
0,794.625,814.5417,19.9167,
2.4,814.5833,897.9583,83.375,
0,898,917.9583,19.9583,

7T_MOVIE3_CC2_v2 Video Timing
0,0,19.9583,19.9583,
3.1,20,200.5417,180.5417,
0,200.5833,220.5417,19.9583,
3.2,220.5833,405.0833,184.5,
0,405.125,425.0833,19.9583,
3.3,425.125,629.2083,204.0833,
0,629.25,649.2083,19.9583,
3.4,649.25,791.75,142.5,
0,791.7917,811.5417,19.75,
3.5,811.5833,894.9583,83.375,
0,895,914.9583,19.9583,

7T_MOVIE4_HO2_v2 Video Timing
0,0,19.9583,19.9583,
4.1,20,252.2917,232.2917,
0,252.,272.2917,19.9583,
4.2,272.,502.1667,229.8333,
0,502.2083,522.1667,19.9583,
4.3,522.2083,777.375,255.1667,
0,777.4167,797.5417,20.125,
4.4,797.5833,880.9583,83.375,
0,881,900.9583,19.9583,,Start Frame,End Frame,Total Duration,FPS,URL
7T_MOVIE1_CC1,
Two_Men,0,5858,5859,25,http://vimeo.com/17970306 
Welcome_To_Bridgeville,0,5320,5321,23.98,http://vimeo.com/31318354 
Pockets,0,4513,4514,25,http://vimeo.com/14216866 
Inside_the_Human_Body,0,1530,1531,25,http://vimeo.com/24930096 
Vimeo_Repeat,,,2002,23.98,
,
7T_MOVIE2_HO1,
Inception_1,41843,47285,5443,23.98,
Social_Network_1,24827,31034,6208,23.98,
Ocean's_Eleven_1,9649,15741,6093,23.98,
Vimeo_Repeat,,,2002,23.98,
,
7T_MOVIE3_CC2,
Off_The_Shelf,0,4334,4335,23.98,http://vimeo.com/1157737
1212,0,4429,4430,23.98,http://vimeo.com/47704935 
Mrs_Meyers_Clean_Day,0,4899,4900,23.98,http://vimeo.com/63405160 
Northwest_Passage,0,4277,4278,30,http://vimeo.com/11363537 
Vimeo_Repeat,0,2002,2002,23.98,
,
7T_MOVIE4_HO2,
Home_Alone_1,25448,31024,5577,23.98,
Erin_Brockovich_2,125815,131332,5518,23.98,
Empire_Strikes_Back_1,3625,9750,6126,23.98,
Vimeo_Repeat,,,2002,23.98,
,
,
Vimeo_Repeat,
J.L. Powell 23 Degrees South ,0,596,597,23,http://vimeo.com/33051721 
LXIV,2454,3858,1405,25,http://vimeo.com/19009646

Re: [HCP-Users] HCP lifespan diffusion gradient table

[Elam, Jennifer]

Hi Harith,

You can download the CCF protocol template used for Lifespan which includes the 
diffusion gradient vectors from the link in the sidebar on this page: 
http://protocols.humanconnectome.org/CCF/

Download The CCF Protocol Template - Human Connectome 
Project
protocols.humanconnectome.org
Downloadable scanner protocol for HCP-style image acquisition for CCF studies

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 Akram, Harith 

Sent: Thursday, August 9, 2018 9:59:43 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] HCP lifespan diffusion gradient table

Hi,

We are trying to set up the HCP imaging protocol (used for the lifespan study) 
on our Prisma (+32ch coil).

Is it possible to get the gradient table please?

\\USER\HCP-Lifespan\Lifespan\Session 1\DWI_dir98_AP
TA:5:35 PAT:Off Voxel size:1.5x1.5x1.5 mm Rel. SNR:1.00 :epse

\\USER\HCP-Lifespan\Lifespan\Session 1\DWI_dir98_PA
TA:5:35 PAT:Off Voxel size:1.5x1.5x1.5 mm Rel. SNR:1.00 :epse

\\USER\HCP-Lifespan\Lifespan\Session 1\DWI_dir99_AP
TA:5:38 PAT:Off Voxel size:1.5x1.5x1.5 mm Rel. SNR:1.00 :epse

\\USER\HCP-Lifespan\Lifespan\Session 1\DWI_dir99_PA
TA:5:38 PAT:Off Voxel size:1.5x1.5x1.5 mm Rel. SNR:1.00 :epse

Harith

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Download HCP1200 PTN data

[Elam, Jennifer]

Hi Taicheng,

The only way to download the PTN dataset is through ConnectomeDB using Aspera, 
which was not affected by the AWS bucket migration. It sounds like the problem 
is your firewall. Our Aspera server is configured to use TCP and UDP Port 33001 
for  file transfers instead of a common port such as Port 22. If you are  
downloading from behind an institutional firewall, please speak with  your IT 
people to ensure that Port 33001 is open to both TCP and UDP  traffic. You also 
might try downloading the dataset from home where you are likely to not have a 
firewall that presents a problem.


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 taicheng_huang 

Sent: Thursday, August 9, 2018 5:11:40 AM
To: hcp-users
Subject: [HCP-Users] Download HCP1200 PTN data

Dear HCP experts,

I would like to download HCP1200 PTN data from ConnectomeDB 
(https://db.humanconnectome.org/data/projects/HCP_1200). After configuring IBM 
Aspera Connect, I couldn't establish HTTP connection. The error message 
reported 'Error establishing HTTP conn... (check HTTP port and firewall)'. I 
also tried to use HTTP proxy for downloading this data but we still couldn't 
establish HTTP connection. I'm wondering if it's due to the recent data 
migration activity. Or could I download the HCP1200 PTN in other ways?
Thanks in advance!

Best,
Taicheng

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] help with setup and analysis

[Elam, Jennifer]

Hi Omri,

Once you login to your ConnectomeDB account and have signed the HCP Open Access 
Data use terms, you can download the neuroimaging data for individuals or 
groups of subjects in packages and the personality measures as part of the 
Behavioral CSV that is available on the Subject Dashboard or the S1200 Release 
Project Page.


See pp.24-30 of the S1200 Release 
Manual
 for basic instructions on navigating the database and downloading data, and 
the rest of the Release Manual for lots of info on the behavioral measures, 
other available data, and more.


Others on the list will best give you advice on setting up a correlational 
analysis.


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 Gillath, Omri 

Sent: Monday, July 30, 2018 1:42:10 PM
To: HCP-Users@humanconnectome.org
Subject: [HCP-Users] help with setup and analysis


Hello everyone,

I’m a new user trying to run some correlations between personality measures and 
existing fMRI data. Would love to get some guidance on how to get access to 
both the fMRI data and the personality measures, and what kind of steps I’ll 
need to make to be able to run correlational analysis? Thanks in advance --Omri



Omri Gillath

Professor

Department of Psychology
University of Kansas
1415 Jayhawk Blvd. Rm 518
Lawrence, Kansas 66045-7556
Phone: 785-864-1772
Fax: 785-864-5696
E-mail: ogill...@ku.edu
Website: http://psych.ku.edu/omri-gillath

Laboratory: http://gillab.ku.edu/

TEDx talk: The Power of (Secure) 
Love



Associate Editor PSPB



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Tractography data for the 1200 subject release

[Elam, Jennifer]

No, HCP has not released tractography on all subjects or produced structural 
connectomes.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Pubuditha Abeyasinghe 
Sent: Monday, July 30, 2018 12:59:56 PM
To: Elam, Jennifer; hcp-users@humanconnectome.org
Subject: Re: Tractography data for the 1200 subject release


Hi Jenn,



Thank you for your reply. Yes, they do contain the preprocessed diffusion data. 
I was just wondering whether they also have the connectomes by any chance (that 
I can’t find out).



Regards,

Pubuditha



From: "Elam, Jennifer" 
Date: Monday, July 30, 2018 at 1:50 PM
To: Pubuditha Abeyasinghe , "hcp-users@humanconnectome.org" 

Subject: Re: Tractography data for the 1200 subject release



Hi Pubuditha,

1200 Subjects release contains updated preprocessed and FSL's 
bedpostX-processed 3T diffusion data on all subjects, which should get you part 
of the way toward your goal.



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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>





From: hcp-users-boun...@humanconnectome.org 
 on behalf of Pubuditha Abeyasinghe 

Sent: Monday, July 30, 2018 12:38:51 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Tractography data for the 1200 subject release



Hi HCP experts,



I am starting to work with the data from 1200 subject release.

I want to generate the connectome for all the subjects by applying tractography 
to the DTI data. It takes a fairly long time to deal with all the subjects. So 
I was wondering whether anyone has done this and published their work or 
whether the connectome data can be found in the HCP data base it self.



Your help is much appreciated!



Regards,

Pubuditha



[Image removed by sender. Western University]
Pubuditha Abeyasinghe
PhD Candidate
Department of Physics and Astronomy

Brain and Mind Institute
Western University
London, ON, Canada
email: pabey...@uwo.ca

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Tractography data for the 1200 subject release

[Elam, Jennifer]

Hi Pubuditha,

1200 Subjects release contains updated preprocessed and FSL's 
bedpostX-processed 3T diffusion data on all subjects, which should get you part 
of the way toward your goal.


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 Pubuditha Abeyasinghe 

Sent: Monday, July 30, 2018 12:38:51 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Tractography data for the 1200 subject release


Hi HCP experts,


I am starting to work with the data from 1200 subject release.

I want to generate the connectome for all the subjects by applying tractography 
to the DTI data. It takes a fairly long time to deal with all the subjects. So 
I was wondering whether anyone has done this and published their work or 
whether the connectome data can be found in the HCP data base it self.


Your help is much appreciated!


Regards,

Pubuditha


[Western University]
Pubuditha Abeyasinghe
PhD Candidate
Department of Physics and Astronomy
Brain and Mind Institute
Western University
London, ON, Canada
email: pabey...@uwo.ca

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Working Memory Recognition Task

[Elam, Jennifer]

Hi Briana,

The last line of this paragraph on p. 50 of the Reference 
Manual
 answers your question:


Recognition Memory

After participants exit the scanner from the session that includes the working 
memory tasks,
they are given a Remember, Know, New  item recognition test for the faces and 
places that were
presented during the working memory task.  Responses to this recognition memory 
test can be
used to create events to analyze the working memory trials as a function of 
whether the item
was subsequently recognized (remember or know) or not (new).  This is referred 
to as a
subsequent memory analysis.
The REC_run1_TAB.txt and REC_run2_TAB.txt files needed for this analysis are in 
the {Subject_ID}/MNINonLinear/Results/tfMRI_WM_LR/ and 
{Subject_ID}/MNINonLinear/Results/tfMRI_WM_RL/ data directories.

So, you will need to look in the WM tfMRI data itself for the subjects you are 
interested in to see which of the WM stimuli the individuals remembered post 
scan.

Greg Burgess may be able to elaborate more if you have further questions.

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 Briana Last 

Sent: Monday, July 23, 2018 7:21:12 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Working Memory Recognition Task

Hi all,

I apologize if this question has been asked already, but I noticed in the HCP 
manual that there is a description of a Recognition task that is administered 
outside of the scanner after the Working Memory (2-Back) task is administered 
in the scanner. Is this task data available? I can't seem to find the data in 
the data dictionary or in any of the datasets, but maybe I'm looking in the 
wrong place...

Thanks in advance!

--
Briana Shiri Last, M.A.
Ph.D Candidate in Clinical Psychology
University of Pennsylvania
425 S. University Avenue
Philadelphia PA, 19104



PRIVACY STATEMENT
The information contained in this e-mail message is intended only for the 
personal and confidential use of the recipient(s) named above. If the reader of 
this message is not the intended recipient or an agent responsible for 
delivering it to the intended recipient, you are hereby notified that you have 
received this document in error and that any review, dissemination, 
distribution, or copying of this message is strictly prohibited. If you have 
received this communication in error, please notify us immediately by e-mail, 
and delete the original message. Thank you!

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Movie tasks fMRI

[Elam, Jennifer]

Hi Michel,

The Movie stimulus files used for 7T are available on the S1200 Project page in 
ConnectomeDB under "Task 
Resources". See more info on the 7T movie watching experiment on pp.59-61 of 
the S1200 Reference 
Manual.


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 Michel Thiebaut 

Sent: Friday, July 27, 2018 8:36:02 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Movie tasks fMRI

Dear HCP Experts,

I was wondering whether you would have the kindness to provide me with a link 
to download/watch the movies used for the movie tasks at 7T.

Thank a lot for your time,
Kind regards

michel

Michel Thiebaut de Schotten
Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Accessing 7T data in the temporary s3 bucket

[Elam, Jennifer]

Hi John,
Actually, the 7T HCP data is not available on AWS S3 yet due to changes in the 
AWS public access program that have necessitated a switchover to a new HCP AWS 
account and the creation of the temporary hcp-openaccess-temp S3 bucket. Once 
we have the hcp-openaccess S3 bucket back up under our new account, we will 
sync the 7T data and announce that it is available. Moving all the data takes a 
lot of time, so please bear with us!

Thanks,
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 Rodgers-Lee, John 
(NIH/NIMH) [C] 
Sent: Friday, July 27, 2018 1:32:54 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Accessing 7T data in the temporary s3 bucket


Hi I’m having some issues downloading the 7T data from the temporary s3 bucket.



I expect to be able to find 7T data for the following subjects (among others): 
995174, 100610 and 878877. I cannot see any in the bucket though for example 
when I list the results for each subject with:

aws s3 ls  --recursive 
s3://hcp-openaccess-temp/HCP_1200/995174/MNINonLinear/Results



If anyone figures out what I’m doing wrong your help would be greatly 
appreciated.



Regards,



John



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] mounting temp bucket

[Elam, Jennifer]

Hi Daniel,

I asked Tim Coalson if he had any advice for you and he replied with the 
following in case it helps you in solving the problem:



On Wed, Jul 18, 2018 at 10:05 PM, Timothy Coalson 
mailto:tsc...@mst.edu>> wrote:
After some quick attempts at s3fs, I am also getting this error.  I think the 
s3fs tools (or at least the version packaged in ubuntu 16.04) and the temporary 
bucket are not compatible for some reason.  Maybe installing the latest s3fs 
from github would help?  Not clear why it would have worked for the old bucket, 
though.

Tim


After trying this with the latest github release of s3fs (but the default 
ubuntu 16.04 fuse), I still get this error.

Here is a probably related open bug on the s3fs tools:

https://github.com/s3fs-fuse/s3fs-fuse/issues/721
[https://avatars2.githubusercontent.com/u/2044211?s=400=4]

Invalid credentials (working in s3cmd) · Issue #721 · s3fs 
...
github.com
I'm using the same IAM credentials on the same machine with s3cmd and it is 
working with normal access, but when using s3fs get invalid credentials message.


If I use the url option, it changes behavior, but doesn't show any contents - 
the curl debug info indicates it tries to redirect back to the default of 
us-east-1 anyway.

Tim


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 King, Daniel (Research 
Student) 
Sent: Wednesday, July 18, 2018 5:13:52 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] mounting temp bucket

Hi HCP-list,

I just wanted to inquire about the temp bucket location for the HCP data. I 
have previously been mounting the bucket data via s3fs with FUSE. However, 
since it has been migrated over to the temp bucket, I can no longer do so? I 
have regenerated the credentials (via connctomeDB) and am using a syntax 
identical to that which I used previously. Is there any advice you could give? 
Due to the timing of the issue I assume it is an issue with the bucket rather 
than s3fs etc. This is the syntax I am using and the subequent output by s3fs, 
it seems to not be finding the bucket.

s3fs -f -o use_cache=~/tmp/cache_s3,uid=119393,gid=500,umask=0,retries=5 
hcp-openaccess-temp:/HCP_1200 ~/OpenData

[CRT] s3fs_init(3294): init v1.79(commit:unknown) with GnuTLS(gcrypt)
[CRT] s3fs_check_service(3711): bucket not found - result of checking service.

However, If I remove the HCP_1200 path and just leave the name of the bucket I 
just get the following :

s3fs -f -o use_cache=~/tmp/cache_s3,uid=119393,gid=500,umask=0,retries=5 
hcp-openaccess-temp ~/OpenData
[CRT] s3fs_init(3294): init v1.79(commit:unknown) with GnuTLS(gcrypt)
[CRT] s3fs_check_service(3707): invalid credentials - result of checking 
service.

Any help would be greatly appreciated!

Best wishes

Daniel King

PhD Candidate in Neurosciences,
School of Life and Health Sciences,
Aston University

Email: kin...@aston.ac.uk
Twitter: @danieljking8


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] questions about the out-scanner NIH Processing speed task

[Elam, Jennifer]

Hi Xinyang,


From the NIH Toolbox website: Some PROMIS domains (processing speed is a PROMIS 
measurement) have multiple versions of instruments (i.e. v1.0, v1.1, v2.0). 
Generally, it is recommended that you use the most recent version available 
which can be identified as the instrument with the highest version number. In 
most cases, an instrument that has a decimal increase (v1.0 to v1.1) retains 
the same item-level parameters as well as instrument reliability and validity.


From the Processing Speed Test description in the NIH Toolbox Scoring and 
Interpretation Manual 
9-27-12 (versions that 
were used for HCP Young Adult):

Scoring Process: The participant’s raw score is the number of items answered 
correctly in a 90-second period, with a range of 0-130. This score is then 
converted to the Toolbox normative scale scores.


With that information, I would say that the difference between v1.0 and 1.1 is 
probably not consequential and the reason that you see a range of numbers of 
trials for the subjects is that they completed a different number of items 
within the 90 second measurement period.


If you want more information, you will have to contact the NIH Toolbox support 
team at h...@nihtoolbox.org or perhaps their support is now fully switched over 
to h...@healthmeasures.net.


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 Xinyang Liu 

Sent: Friday, July 6, 2018 5:52 AM
To: HCP 讨论组
Subject: [HCP-Users] questions about the out-scanner NIH Processing speed task

Dear HCP experts,

Hi. We are currently looking at the out-scanner behavioral data. There are two 
questions about the NIH Processing speed task:

1. In the Processing speed raw data, there are two similar task names. One is 
"NIH TB Pattern Comparison Processing Speed Age 7+", the other is "NIH TB 
Pattern Comparison Process Speed 7+ v 1.1". Could you please tell whether these 
two groups of measurements are the same for this task?

2. Also in this task, we found that the trial number varies a lot across 
participants, not like in other tasks where the trial numbers are consistently 
the same within one task. Could we ask why?

Any of your kind guidance would be very appreciated. Thank you very much.

Best regards,
Xinyang







___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP AWS data moving to temporary bucket location on July 5th, 2018

[Elam, Jennifer]

Attention all users of HCP Data in our Amazon Web Services (AWS) S3 Bucket:

Recent changes in the AWS Public Dataset Program have required migration of HCP 
data stored in AWS S3 to a new account.  As part of this transition, we must 
temporarily disable access to the current s3://hcp-openaccess/ bucket and make 
the data available through a temporary bucket location 
(s3://hcp-openaccess-temp/).  It is expected that the migration may take 4 – 6 
weeks.  During this time, data will be available via the temporary bucket 
location.



Once the original bucket has been fully migrated to the new account, we will 
announce that the migration is complete and you will once again access the data 
via the original bucket (s3://hcp-openaccess).  We anticipate transition to the 
temporary bucket to occur this Thursday, July 5th, 2018.  This change will 
require you to regenerate your AWS credentials via ConnectomeDB.  Once this 
change occurs, you will see a message on the ConnectomeDB login page that 
notifies of the change and will also receive notification of the new, temporary 
bucket as you recreate your credentials (access keys).



There may be a short time; several hours to a day or so, where the original 
bucket still works with your existing access keys.  Soon thereafter, however, 
access to the s3://hcp-openaccess bucket will be removed so that the bucket can 
be transitioned to the new account.



Let us know if you have any questions and thank you for your patience during 
this transition.



Best,

HCP Staff

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

[Elam, Jennifer]

HI Xinyang,

Yes, those in your list are definitely the Retest subjects. You'd probably want 
to use the first set if you are using other data for those subjects that was 
collected for the first (test) timepoint so that you don't introduce a possible 
systematic bias for the retest subjects.


Some subjects might not have all the data for all the different behavioral 
tests or imaging modalities for a wide variety of reasons. In general, we make 
the data we have available, even if incomplete.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Xinyang Liu 
Sent: Friday, June 29, 2018 6:38:24 AM
To: Elam, Jennifer
Cc: HCP 讨论组
Subject: Re: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

Dear Jennifer,

Thanks a lot for your reply. So in this case, either set is ok to use, right? :)

Please find the subID list of the DCCS task attached. Apart from that, there is 
also a subject (No.341935) with 2 trials and a subject (No.638049) with 27 
trials.


Best regards,
Xinyang



At 2018-06-29 19:09:53, "Elam, Jennifer"  wrote:

Can you share a list of subjects where you see 60 trials for the DCCS task? 
Likely these subjects are HCP Retest subjects who went through the entire 
protocol twice (about 6 months or so between acquisitions, depending on the 
subject) and therefore have two sets of responses/imaging datasets.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Sent: Friday, June 29, 2018 3:50:06 AM
To: HCP 讨论组
Subject: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

Dear HCP experts,

Hi. We are looking at the HCP battery of behavioral measures. We found that in 
the recordings of individual performances, there are some participants who 
repeated the task for a second time. For example, in the Executive Function  
DCCS task (on manual page 183), there are 30 experimental trials apart from the 
practice part. However, the excel recording shows that some participants 
finished 60 trials. We would like to know what was the situation and does it 
mean the first round of measurement invalid? Thanks a lot.

Best regards,
Xinyang






___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

[Elam, Jennifer]

Can you share a list of subjects where you see 60 trials for the DCCS task? 
Likely these subjects are HCP Retest subjects who went through the entire 
protocol twice (about 6 months or so between acquisitions, depending on the 
subject) and therefore have two sets of responses/imaging datasets.


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 Xinyang Liu 

Sent: Friday, June 29, 2018 3:50:06 AM
To: HCP 讨论组
Subject: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

Dear HCP experts,

Hi. We are looking at the HCP battery of behavioral measures. We found that in 
the recordings of individual performances, there are some participants who 
repeated the task for a second time. For example, in the Executive Function  
DCCS task (on manual page 183), there are 30 experimental trials apart from the 
practice part. However, the excel recording shows that some participants 
finished 60 trials. We would like to know what was the situation and does it 
mean the first round of measurement invalid? Thanks a lot.

Best regards,
Xinyang






___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--- Begin Message ---
Dear HCP experts,


Hi. We are looking at the HCP battery of behavioral measures. We found that in 
the recordings of individual performances, there are some participants who 
repeated the task for a second time. For example, in the Executive Function  
DCCS task (on manual page 183), there are 30 experimental trials apart from the 
practice part. However, the excel recording shows that some participants 
finished 60 trials. We would like to know what was the situation and does it 
mean the first round of measurement invalid? Thanks a lot.


Best regards,
Xinyang 


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
--- End Message ---

[HCP-Users] Workbench v1.3.1 Released - a few bug fixes and new features

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
June 5, 2018
Connectome Workbench v1.3.1 Released
Announcing version 1.3.1 of Connectome 
Workbench 
(WB) brain visualization and analysis software, which fixes a few bugs and adds 
a few features from the recent v1.3.0 release, is now available for 64-bit Mac 
OSX, Windows, and Linux. The Workbench distribution includes wb_view, a 
GUI-based visualization platform, and wb_command, a command-line program for 
performing a variety of algorithmic tasks using volume, surface, and 
grayordinate data.
Changes in Workbench v1.3.1
wb_view:
New Features

  *   Scene numbers using a file added next to files in scene "list files" 
window
  *   Scenes "replace all" no longer shows tab highlight outline in captured 
previews
  *   Builds with older QT5 no longer have very large overlay toolbox by default


Bug Fixes

  *   fixed wb_view crash when loading label volumes
  *   Settings synchronized across overlay settings windows that refer to the 
same file


wb_command:
New Features

  *   -*-roi-from-extrema commands give warnings when output has no maps
  *   -volume-set-space now has a -file option to take space information from 
another volume
  *   -volume-math copies timestep from input files


Bug Fixes

  *   bash completion for wb_shortcuts should now work reliably
  *   wb_shortcuts -cifti-demean should not give warnings about extensions for 
temporary files

Installation for improved tab completion for wb_command:
The below instructions are OPTIONAL, they are not required for workbench to 
function properly.  They are intended for users that use wb_command manually in 
the bash shell.

These instructions are only for people who downloaded workbench as a zip file, 
installation through a package manager such as neurodebian performs similar 
steps automatically.

For relatively modern versions of the "bash" shell, workbench now provides tab 
completions for wb_command options and file extensions (the default OS X bash 
is too old, you would need to use homebrew, macports, or similar).

The easiest way to install them is to copy the file "bashcomplete_wb_command" 
from the workbench folder into /etc/bash_completion.d/, if you have admin 
rights.  If you do not have admin rights, you can make a copy of 
"bashcomplete_wb_command" in your home directory, but renamed to 
".bash_completion" (the dot on the front is important).  Ignore the 
"bashcomplete_wb_shortcuts" file, the wb_shortcuts completions are also inside 
the "bashcomplete_wb_command" file.  The file is located here, depending on OS:

Ubuntu/Debian Linux: workbench/exe_linux64/bashcomplete_wb_command
Centos/RedHat Linux: workbench/exe_rh_linux64/bashcomplete_wb_command
Windows: workbench/bin_windows64/bashcomplete_wb_command
OS X: workbench/macosx64_apps/bashcomplete_wb_command

Once this is done, open a NEW terminal window, type "wb_command -file-info" but 
don't press enter, instead press tab, and the line should change to "wb_command 
-file-information".  If it does not, then it is likely that the OS's 
"bash-completion" package is not installed.


WB v1.3.1 is compatible with the WB v1.0 tutorial and the processed 1200 
Subjects Group Average Data available to download at 
http://humanconnectome.org/connectome/get-connectome-workbench.html and on the 
 ConnectomeDB HCP project 
page. Access to both 
datasets require ConnectomeDB login and signature of the HCP Open Access Data 
Use Terms.

To download the  WB v1.3.1 
source code from GitHub: 
follow the link, click Releases (near the top center of the page), then under 
v1.3.1, click the “Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to 
the hcp-users discussion list (sign up 
here).

Best,
The WU-Minn HCP Consortium

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Spaces added, register today for HCP Course 2018!

[Elam, Jennifer]

If you are considering joining us for the 2018 HCP Course: "Exploring the Human 
Connectome" June 25 – 29 at the University of Oxford, a 
few additional lodging rooms at Worcester College have opened up for just $675 
for 6 nights, first come first served.  For more info and to register visit the 
HCP Course 2018 
website.
 We will continue to take registrations for the course until our venue at the 
Blavatnik School of Government is full.
HCP Course 2018 is a 5-day intensive course of lectures and hands-on practicals 
and your best opportunity to learn directly from HCP investigators and gain 
practical experience with the Human Connectome Project's data and approach to 
multimodal whole brain imaging, processing and analysis and to get up to speed 
on HCP tools including Connectome 
Workbench 
(v1.3.0 just released!) and sharing your own analyzed imaging datasets via the 
BALSA database.
If you have any questions, please contact us at: 
hcpcou...@humanconnectome.org

We look forward to seeing you in Oxford!

Best,
2018 HCP Course Staff

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Elam, Jennifer]

What browser are you using?

Thanks,
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: Michel Thiebaut <michel.thieb...@gmail.com>
Sent: Friday, May 25, 2018 1:44:34 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Experiencing downloading problems

Hi Jenn,

I tried again this morning on two computers.
I'm afraid it still doesn't work.

Best

mich

Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60<tel:%2B33%207%2083%2050%2081%2060>
http://www.bcblab.com
http://toolkit.bcblab.com


On Thu, May 24, 2018 at 3:33 PM, Elam, Jennifer 
<e...@wustl.edu<mailto:e...@wustl.edu>> wrote:
Hi Mich,
We believe the issue should be resolved now,  please try the download again. 
Thanks for your patience!

Best,
Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 
8108<https://maps.google.com/?q=8108+%0D%0A660+South+Euclid+Avenue+%0D%0ASt.+Louis,+MO+63110+%0D%0A314=gmail=g>
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org>


From: Michel Thiebaut 
<michel.thieb...@gmail.com<mailto:michel.thieb...@gmail.com>>
Sent: Thursday, May 24, 2018 1:39:11 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>

Subject: Re: [HCP-Users] Experiencing downloading problems

Hi Jenn,

Thanks for getting back to me. I tried to download a single subject this 
morning again on two different computers that I previously used to download HCP 
data, and it didn't work.
The download just doesn't start in Aspera.

Thanks for letting me know when the redeployment is done.

Kind regards

mich

Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de 
l'Hôpital<https://maps.google.com/?q=47+Bvd+de+l'H%C3%B4pital=gmail=g>
 CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60<tel:%2B33%207%2083%2050%2081%2060>
http://www.bcblab.com
http://toolkit.bcblab.com


On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer 
<e...@wustl.edu<mailto:e...@wustl.edu>> wrote:

Hi again Mich,

Go ahead and try a test download, but the developers here have found another 
issue that might be causing the problem. For their fix to go through they need 
to schedule a redeployment of ConnectomeDB, which will hopefully happen 
tomorrow. Sorry for the delay.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Elam, Jennifer <e...@wustl.edu<mailto:e...@wustl.edu>>
Sent: Wednesday, May 23, 2018 11:32:18 AM
To: Michel Thiebaut; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Experiencing downloading problems


Hi Mich,

Could you try the download again? We had an outage earlier this morning, but we 
are hoping that everything is working now. Let us know how it goes.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Michel Thiebaut 
<michel.thieb...@gmail.com<mailto:michel.thieb...@gmail.com>>
Sent: Wednesday, May 23, 2018 4:56:46 AM
To: hcp-users@humanconnectome.org<mailto:hcp-user

Re: [HCP-Users] Downloading tutorial data

[Elam, Jennifer]

Hi Mahinda,

Can you clear the Safari browser's cache and try again? You could also try a 
different browser. Hopefully that will do the trick.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Mahinda Yogarajah <mahin...@doctors.org.uk>
Sent: Thursday, May 24, 2018 8:59:03 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Downloading tutorial data

Hi,

Thanks for the quick reply. I just tried it again, but it is still hanging.

Thanks,

Mahinda

On 24 May 2018, at 14:45, Elam, Jennifer 
<e...@wustl.edu<mailto:e...@wustl.edu>> wrote:

Hi Mahinda,
We had an issue with our download server that we just resolved, so please try 
your download again.

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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org>


From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Mahinda Yogarajah 
<mahin...@doctors.org.uk<mailto:mahin...@doctors.org.uk>>
Sent: Thursday, May 24, 2018 5:25:42 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] Downloading tutorial data

Dear All,

I am having downloading the tutorial dataset from the HCP website.

I am using Safari v11.1 and I have Aspera connect installed in the browser. The 
Aspera connect is working as I can download test files from the Aspera website 
using the tool.

When I click on the tutorial data download link it takes me to the download 
resource launcher and then hangs. Clicking on the “click here” link for 
downloads taking time also does not work.

Any advice gratefully received.

Thanks,

Mahinda


___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Downloading tutorial data

[Elam, Jennifer]

Hi Mahinda,
We had an issue with our download server that we just resolved, so please try 
your download again.

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 Mahinda Yogarajah 

Sent: Thursday, May 24, 2018 5:25:42 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Downloading tutorial data

Dear All,

I am having downloading the tutorial dataset from the HCP website.

I am using Safari v11.1 and I have Aspera connect installed in the browser. The 
Aspera connect is working as I can download test files from the Aspera website 
using the tool.

When I click on the tutorial data download link it takes me to the download 
resource launcher and then hangs. Clicking on the “click here” link for 
downloads taking time also does not work.

Any advice gratefully received.

Thanks,

Mahinda


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Elam, Jennifer]

Hi Mich,
We believe the issue should be resolved now,  please try the download again. 
Thanks for your patience!

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: Michel Thiebaut <michel.thieb...@gmail.com>
Sent: Thursday, May 24, 2018 1:39:11 AM
To: Elam, Jennifer
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Experiencing downloading problems

Hi Jenn,

Thanks for getting back to me. I tried to download a single subject this 
morning again on two different computers that I previously used to download HCP 
data, and it didn't work.
The download just doesn't start in Aspera.

Thanks for letting me know when the redeployment is done.

Kind regards

mich

Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60<tel:%2B33%207%2083%2050%2081%2060>
http://www.bcblab.com
http://toolkit.bcblab.com


On Wed, May 23, 2018 at 11:10 PM, Elam, Jennifer 
<e...@wustl.edu<mailto:e...@wustl.edu>> wrote:

Hi again Mich,

Go ahead and try a test download, but the developers here have found another 
issue that might be causing the problem. For their fix to go through they need 
to schedule a redeployment of ConnectomeDB, which will hopefully happen 
tomorrow. Sorry for the delay.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Elam, Jennifer <e...@wustl.edu<mailto:e...@wustl.edu>>
Sent: Wednesday, May 23, 2018 11:32:18 AM
To: Michel Thiebaut; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Experiencing downloading problems


Hi Mich,

Could you try the download again? We had an outage earlier this morning, but we 
are hoping that everything is working now. Let us know how it goes.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Michel Thiebaut 
<michel.thieb...@gmail.com<mailto:michel.thieb...@gmail.com>>
Sent: Wednesday, May 23, 2018 4:56:46 AM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: [HCP-Users] Experiencing downloading problems

Dear HCP team,

I've been experiencing downloading issue today.
I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), however, 
for some reason, the download doesn't start in Aspera. I also tried a single 
subject without success.
I usually have no problem.
Is it happening on your side?

Thanks a lot for letting me know
Kind regards

mich


Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de 
l'Hôpital<https://maps.google.com/?q=47+Bvd+de+l'H%C3%B4pital=gmail=g>
 CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60<tel:%2B33%207%2083%2050%2081%2060>
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Elam, Jennifer]

Hi again Mich,

Go ahead and try a test download, but the developers here have found another 
issue that might be causing the problem. For their fix to go through they need 
to schedule a redeployment of ConnectomeDB, which will hopefully happen 
tomorrow. Sorry for the delay.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Elam, Jennifer 
<e...@wustl.edu>
Sent: Wednesday, May 23, 2018 11:32:18 AM
To: Michel Thiebaut; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Experiencing downloading problems


Hi Mich,

Could you try the download again? We had an outage earlier this morning, but we 
are hoping that everything is working now. Let us know how it goes.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Michel Thiebaut 
<michel.thieb...@gmail.com>
Sent: Wednesday, May 23, 2018 4:56:46 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Experiencing downloading problems

Dear HCP team,

I've been experiencing downloading issue today.
I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), however, 
for some reason, the download doesn't start in Aspera. I also tried a single 
subject without success.
I usually have no problem.
Is it happening on your side?

Thanks a lot for letting me know
Kind regards

mich


Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60<tel:%2B33%207%2083%2050%2081%2060>
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Experiencing downloading problems

[Elam, Jennifer]

Hi Mich,

Could you try the download again? We had an outage earlier this morning, but we 
are hoping that everything is working now. Let us know how it goes.


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 Michel Thiebaut 

Sent: Wednesday, May 23, 2018 4:56:46 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Experiencing downloading problems

Dear HCP team,

I've been experiencing downloading issue today.
I tried to download the 7T Resting-State fMRI FIX-Denoised (Extended), however, 
for some reason, the download doesn't start in Aspera. I also tried a single 
subject without success.
I usually have no problem.
Is it happening on your side?

Thanks a lot for letting me know
Kind regards

mich


Michel Thiebaut de Schotten
Associate Professor, PhD, HDR, CNRS
Sorbonne Universities, UPMC Univ Paris 06
Brain Connectivity and Behaviour Group
Frontlab, Institut du cerveau et la moelle épinière
Hôpital de la Salpêtrière - ICM
47 Bvd de l'Hôpital CS21414
75646 PARIS CEDEX 13

Skype: michel_thiebaut_de_schotten
phone: +33 7 83 50 81 60
http://www.bcblab.com
http://toolkit.bcblab.com


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] sharing of statistics from HCP analysis

[Elam, Jennifer]

Hi Joseph,

As long as the data you are sharing doesn't list restricted data for individual 
subjects (that could be used to identify subjects) it should be fine to share 
per our data use terms.


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 Joseph Orr 

Sent: Monday, May 21, 2018 10:19:11 AM
To: HCP Users
Subject: [HCP-Users] sharing of statistics from HCP analysis

I previously published an analysis of the effects of marijuana use in the HCP 
sample. A group of researchers has contacted me asking for means and standard 
deviations from my analyses for use in a meta-analysis. I wanted to confirm 
that sharing this data doesn't violate the data use agreement. I'm assuming it 
doesn't since I could have reported this information in the paper.

Thanks

--
Joseph M. Orr, Ph.D.
Assistant Professor
Department of Psychological and Brain Sciences
Texas A Institute for Neuroscience
Texas A University
College Station, TX

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

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

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] question about link to behavioural measures docs

[Elam, Jennifer]

Hi Joelle,

Please download and use the spreadsheet versions of the Data Dictionary 
available at: 
https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Dictionary+Public-+Updated+for+the+1200+Subject+Release


Also, for citations please refer to Chapter 5: Behavioral and Individual 
Difference Measures Details (starting on p. 187) of the HCP S1200 Release 
Reference 
Manual.


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 Joelle Zimmermann 

Sent: Tuesday, May 15, 2018 9:31:22 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] question about link to behavioural measures docs

Hi HCPers,

I am looking for a link to the documentation for citation for the following 
behavioural measures (see below). I had been referring to the following link, 
but it looks like that is now expired:
https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Dictionary+Public-+500+Subject+Release

I found also the following, however, this doesn't seem to include documentation 
for all of the measures:
https://wiki.humanconnectome.org/display/PublicData/HCP+Data+Dictionary+Public-+Updated+for+the+1200+Subject+Release

Any pointers would be much appreciated.

Thanks,
Joelle


ListSort_AgeAdj
PicSeq_AgeAdj
CardSort_AgeAdj
Flanker_AgeAdj
ProcSpeed_AgeAdj
WM_Task_2bk_Acc
WM_Task_2bk_Median_RT
WM_Task_0bk_Acc
WM_Task_0bk_Median_RT
PMAT24_A_CR
PMAT24_A_RTCR

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Reminder to Register for HCP Course 2018

[Elam, Jennifer]

Only a few weeks until 2018 HCP Course: "Exploring the Human Connectome" in 
Oxford, UK!  For more info and to register visit the HCP Course 2018 
website.
A limited number of registrations with accommodation at Worcester College 
included are available until filled, or May 29 at the latest.
HCP Course 2018 will be held June 25 – 29 at the Blavatnik School of 
Government, at the University of Oxford. The 5-day intensive course of lectures 
and hands-on practicals is a great opportunity to learn directly from HCP 
investigators and gain practical experience with the Human Connectome Project's 
data and approach to multimodal whole brain imaging, processing and analysis.
The course is also a great way to get up to speed on HCP tools including 
Connectome 
Workbench 
(v1.3.0 just released!) and sharing your own analyzed imaging datasets via the 
BALSA database.
If you have any questions, please contact us at: 
hcpcou...@humanconnectome.org

We look forward to seeing you in Oxford!

Best,
2018 HCP Course Staff


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Help with Q13 acquisition subjects structural data download?

[Elam, Jennifer]

Hi Magda and Thomas,

Our Aspera server went down over the weekend. Please try your download again 
and let us know if you continue to have errors.


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 Magda Tsintou 

Sent: Saturday, May 12, 2018 11:19:25 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Help with Q13 acquisition subjects structural data 
download?

Dear HCP community,

I am sending you this email because I have been trying the last couple of days 
to download the structural preprocessed and structural extended preprocessed 
files of a couple of subjects from the Q13 acquisition (in particular 102109 
and 103212; I honestly did not attempt more at that point) and, even though I 
had no issues downloading the diffusion data from the same subjects, I could 
not download any structural data.

I am working on a Mac laptop and even installed the latest Aspera plugin just 
in case this was the issue but the error I receive is: "Error: Server aborted 
session: Failed to connect to management socket (Code: 16)".

Can anyone here help me troubleshoot? I really need those files for a new 
project the soonest possible. Thank you very much.

Best regards,
Magda.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] WB v1.3.0 Released!

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
May 8, 2018
Connectome Workbench v1.3.0 Released
The WU-Minn HCP Consortium is pleased to announce that version 1.3.0 of 
Connectome 
Workbench 
(WB) brain visualization and analysis software is now available for 64-bit Mac 
OSX, Windows, and Linux. The Workbench distribution includes wb_view, a 
GUI-based visualization platform, and wb_command, a command-line program for 
performing a variety of algorithmic tasks using volume, surface, and 
grayordinate data.

Notable changes in WB v1.3.0 include:
wb_view:
Best Practices Guide for creating Annotations and Scenes added to Help

Charting

  *   Chart View fully revised to include a layer-like system and support for 
histograms and for charts from many more file types.
  *   Improved and expanded options for control of axes.
  *   Old version of charting remains for compatibility with older scenes.

Annotations

  *   Improved aspect locking with notifications
  *   Warn if annotation text is too small
  *   Added new coordinate space for adding annotations in the new version of 
charting
  *   Line thickness maximum removed and line thickness scales with tab height

BALSA compatibility (BALSA =  Brain Analysis Library 
of Spatial Maps and 
Atlases
 database for sharing analyzed data as WB scenes)

  *   Improved dialog for uploading scene file to BALSA with ability to create 
and edit BALSA study names
  *   Scene Identifiers are requested from BALSA and added to the scene file 
after successful upload of a scene file to BALSA
  *   Added automatic detection of the base path (for recreating directory 
structure of shared datasets)


Scenes

  *   Scenes window revised, including ability to save scene files directly 
without using Save/Manage Files
  *   Added List Files... button to show all data files referenced by a scene 
file
  *   Scenes reload a file if the version on disk has been modified since 
loaded into memory
  *   Warn if there are modified files prior to loading a scene
  *   Volume attributes (crosshairs, labels, etc.) are saved to scenes


Volumes

  *   Volume surface outline scales with tab height
  *   Improved sform support of non LPI oriented files
  *   Warn if a NIFTI volume file contains invalid qform and sform
  *   Added masking option for oblique slice drawing so that edge effects from 
cubic interpolation can be hidden



Miscellaneous

  *   Reading of GIFTI RGBA files is now supported
  *   Upgraded to Qt 5.7 and compilers that support C++11.  Using Qt 5.7 may 
help with some "XCB errors" encountered on Linux.

Overlay Settings

  *   Added thresholding of Overlay Layers using data from another data file 
and map
  *   Added inversion of Palettes for brainordinate coloring

wb_command:
Changes to existing behavior:

  *   corrected qform calculation in oblique or unusual orientation volume files
  *   built against QT5, on newer OSes for mac and linux
  *   surface to volume mapping defaults have changed for less overshoot and 
sharper results (volume to surface defaults are unchanged, but has option 
available for sharper results)
  *   Window->Identify... cifti index now uses 1-based indexing
  *   volume to surface myelin mapping method has been fixed to use the 
cylindrical cutoff described in the paper, with a new option to restore the old 
unintended behavior
  *   -*-stats commands now use multi-map roi files to output multiple columns 
of stats


New notable features:

  *   override map index for yoking group in -show-scene, give error message on 
command failure
  *   tab completion for wb_command (extensive) and wb_shortcuts (basic) in bash
  *   acceleration of correlation by use of SIMD instructions - thanks to 
Kristian Loewe
  *   ability to write smaller low-precision cifti using integer datatypes and 
scaling
  *   new -*-label-probability commands
  *   new strain-based surface and volume distortion measures
  *   generates warnings when writing files with incorrect extensions

Bugfixes:

  *wb_shortcuts concatenate functions don't fail with "unbound variable"
  *   -cifti-merge-dense fixed for volume label data
  *   -cifti-parcel-mapping-to-label help corrected
  *   -cifti-create-dense-from-template handling of -cifti with voxel data
  *   GEO_GAUSS and GEO_GAUSS_EQUAL smoothing methods now use the corrected 
vertex areas in their distance computation (GEO_GAUSS_AREA, the default, 
recommended method, already used them)


WB v1.3.0 is compatible with the WB v1.0 tutorial and the processed 1200 
Subjects Group Average Data available to download at 
http://humanconnectome.org/connectome/get-connectome-workbench.html and on the 
 ConnectomeDB HCP project 

Re: [HCP-Users] Adjusting EV timing text files in EMO task

[Elam, Jennifer]

Hi Michelle,

Greg may want to add more, but I think what you are seeing is related to the 
bug in the Emotion task as described on p54 of the S1200 Release 
Manual:


Note: A bug was written into the E-prime script for the EMOTION task, such that 
the task stopped short of the last three trials of the last task block in each 
run. This bug was not discovered until data had been collected on several 
participants. Consequently, the BOLD images and E-Prime data for the EMOTION 
task are shorter than our original design described above.


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 Michelle Chiu 

Sent: Tuesday, May 1, 2018 3:24:27 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Adjusting EV timing text files in EMO task

Hello all,

I'm a little confused as to whether the timings in the EVs folder 
(fear/neutral.txt) need adjusting? The GLM model .png output for the EMO task 
(attached below) seems to have no padding at the end of the run.
[cid:ii_jgo46pzh0_1631d5a6ceb9bf26]

Any clarification would be much appreciated, thank you!!

-Michelle

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] existing datasets for fmri+diffusion in children through young adults?

[Elam, Jennifer]

Hi Keith,

The PING study might be a possibility, 
although it is a little unclear from their data 
site if the data are still being shared to 
the community for those that don't already have an account on their portal. 
You'll have to write them at p...@ucsd.edu to ask.


Also, some data is now available from 
ABCD. Others on this list 
who have accessed the ABCD data can comment more.


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 Keith Jamison 

Sent: Friday, April 27, 2018 10:18:31 AM
To: HCP Users
Subject: [HCP-Users] existing datasets for fmri+diffusion in children through 
young adults?

Hi HCP-ers,

Does anybody know of any existing publicly available datasets with fMRI and 
diffusion that include ages, say, 8-25?  There are the 27 subjects from the HCP 
Lifespan Pilot (12 of which are in this range), and I know there are a number 
of large studies currently in the acquisition stage still, but are there any 
other studies that have already made data publicly available?

Thanks!
-Keith

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] alcohol dependence measure in the restricted data set

[Elam, Jennifer]

Hi Peter,

  1.  5= Yes, they have met DSM4 criteria for Alcohol Dependence at some point 
over their lifetime (not necessarily at time of SSAGA screen). 1= No, they have 
never met DSM4 criteria for Alcohol Dependence at any point over their 
lifetime. I will add the clarification to the data dictionary.
  2.  Note that the Alcohol Use 7 day retrospective data that the 
Total_Drinks_7days variable comes from was collected at the time of the MRI 
scanning visit. The SSAGA screen was done by phone close to the time of 
confirming study eligibility and consent, which could be weeks or months before 
the actual MRI scanning visit.

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 Manza, Peter (NIH/NIAAA) 
[F] 
Sent: Thursday, April 19, 2018 2:44:09 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] alcohol dependence measure in the restricted data set


Hi all,

I have a question about the "SSAGA_Alc_D4_Dp_Dx" measure in the restricted data 
set. The data dictionary only says "Participant meets DSM4 criteria for DSM4 
Alcohol Dependence", but I'm still wondering about two things:


  1.  It seems participants are scored as either "1" or "5". I'm assuming "5" 
means they do meet the criteria for dependence, and "1" means they do not, is 
this correct?
  2.  If true, the characteristics of this group of subjects look somewhat odd. 
More than a handful report having had 0 drinks in the last 7 days (from the 
"Total_Drinks_7days" measure). It seems unlikely that someone would not have 
drank anything recently but still meet the DSM-IV criteria for alcohol 
dependence. What could be the explanation for this? Missing data? Or does the 
SSAGA_Alc_D4_Dp_Dx include current or PAST history of dependence?

Thanks,
Pete

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Workbench vs 3DSlicer?

[Elam, Jennifer]

Hi Hae-Min,

I can't comment on 3DSlicer, but despite the activity on Github, we continue to 
actively develop new features for Workbench, both for wb_command and the 
wb_view GUI. In fact, we are currently preparing for a v1.3 Workbench release 
to occur in a matter of weeks.


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 Jung, Hae-Min 

Sent: Thursday, April 19, 2018 12:05:17 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Workbench vs 3DSlicer?


Hi All,


Can anyone comment on their experiences between Workbench and 3DSlicer? They 
seem to have very similar uses (including scene file generation).


3DSlicer also seems to have ongoing development on new features, whereas 
Workbench's Github shows mostly bugfixing with no big update since 1.2.3's 
release in August 2016.


Thank you,

Hae-Min Jung

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP Course 2018 at Oxford: Final Course Schedule posted -- Register Now!

[Elam, Jennifer]

Faculty listings and the full schedule of covered 
topics
 are now available for the 2018 HCP Course: "Exploring the Human 
Connectome",
 to be held June 25 – 29, 2018 at the Blavatnik School of 
Government, at the University of 
Oxford, in Oxford, UK!

The 5-day intensive course is a great opportunity to learn directly from HCP 
investigators and gain practical experience with the Human Connectome Project's 
approach to multimodal whole brain imaging acquisition, processing, analysis, 
visualization, and sharing of data and results.

For more info and to register visit the HCP Course 2018 
website.
 Don't delay, registration is limited, and the course is filling up fast! 
Nearby affordable accommodations are available at Worcester College at Oxford 
by selecting registration with accommodations on the site.

If you have any questions, please contact us at: 
hcpcou...@humanconnectome.org

We look forward to seeing you in Oxford!

Best,
2018 HCP Course Staff


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Mismatch in directory structure HCP 1200 subject release

[Elam, Jennifer]

Hi Michelle,

The subjects you listed are all subjects who did not complete the Gambling task 
runs and therefore have no gambling tfMRI data. The "known issues" addressed on 
the wiki do not include listings of data we did not collect on individual 
subjects due to the subject not tolerating the scanner, problems with the data 
that make it unusable, etc. Rather, we list the data available for individual 
subjects with ConnectomeDB with the MRsession* variables and the Study 
Completion variables.


There are filters in the ConnectomeDB Subject Dashboard (click on Explore 
Subjects after logging into db.humanconnectome.org) with which you can find 
subjects that have complete data for the modalities you are interested in 
analyzing. Please see pp. 25-27 of the S1200 Reference 
Manual
 for info on using the filters.


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 Michelle Chiu 

Sent: Tuesday, April 17, 2018 10:20:46 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Mismatch in directory structure HCP 1200 subject release

Hello all,

I was running preprocessing on subjects from HCP 1200 release (gambling task 
specifically) with AWS and noticed the following four subjects in the first 
~200 don’t have the same directory structure as the rest . Everyone else seems 
to have s3/hcp/$subjnum/MNINonLinear/Results/tfMRI_GAMBLING_$run etc
But the following four don’t have a “Results” folder within MNINonLinear for 
either run.

I’ve looked on the HCP wiki and don’t see these subjects among those with known 
issues.

131621
129533
129432
126931

Am I missing something here? Thank you so much!

-michelle

Sent from my iPhone
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Unsubscribe

[Elam, Jennifer]

You are unsubscribed.

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 Erin Defrates 

Sent: Sunday, April 15, 2018 3:41:04 PM
To: HCP-Users@humanconnectome.org
Subject: [HCP-Users] Unsubscribe


Please unsubscribe me from this mailing list, effective immediately.  If there 
is a link I need to use, please send it to me.



Thank you.





Erin DeFrates, PMP

Departmental Systems Administrator (CRM)

Enterprise Resource Planning | Clark County Nevada

500 S Grand Central Parkway, Suite 3012 | Las Vegas, NV 89155

Phone: 702.868.4275

edefra...@clarkcountynv.gov|Internet Web 
Site: http://www.clarkcountynv.gov/





This message is for the sole use of the intended recipient(s) and may contain 
confidential and/or privileged information. Any unauthorized review, use, 
disclosure or distribution is prohibited. If you are not the intended 
recipient, please contact the sender by reply email and destroy all copies of 
the original.



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!

[Elam, Jennifer]

Hi Jenifer,

There isn't a place to register hypotheses on dbGaP that I'm aware. People have 
asked for this for HCP and other shared/open datasets generally, but it would 
be difficult/impossible to scientifically police investigator's claims on a 
hypothesis (who would have the authority to police it? would it be worth the 
effort? lots of philosophical and logistical questions arise..).


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Juranek, Jenifer <jenifer.jura...@uth.tmc.edu>
Sent: Friday, April 13, 2018 11:24:04 AM
To: Elam, Jennifer; hcp-users@humanconnectome.org
Cc: thomas.nich...@bdi.ox.ac.uk
Subject: RE: HCP Young Adult Genetics Data Released on dbGaP!!


Hi Jenn,

Thanks so much for the info.

Do folks register their hypotheses somehow in the dbGaP (transparency and 
reliability measures percolating throughout the research community…particularly 
genetics).

Cheers,

JJ



~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

Jenifer Juranek, PhD

Director of the BRAIN Lab

Associate Professor

Department of Pediatrics

McGovern Medical School

UTHealth

713.500.8233







From: Elam, Jennifer [mailto:e...@wustl.edu]
Sent: Friday, April 13, 2018 11:16 AM
To: Juranek, Jenifer; hcp-users@humanconnectome.org
Cc: thomas.nich...@bdi.ox.ac.uk
Subject: Re: HCP Young Adult Genetics Data Released on dbGaP!!



Hi Jenifer,

I would use the search string: MH091657 OR "Human Connectome Project" to search 
PubMed for manuscripts that have correctly cited the WU-Minn-Oxford HCP grant 
(over 500 to date!).



I am not aware of papers that fit your criteria, but Tom Nichols (CC'd) would 
know what's out there (and likely what's in the pipeline) from some of the 
community.



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<mailto:e...@wustl.edu>
www.humanconnectome.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanconnectome.org_=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=5lTvy6Wg6B_LOeHDopdvHe3rsvrZL4fUVf0hY0invSI=Ni2UWsDUMlmfG5dp9UYsUug5f-sXuQw6O2otLF2YrJw=>





From: Juranek, Jenifer 
<jenifer.jura...@uth.tmc.edu<mailto:jenifer.jura...@uth.tmc.edu>>
Sent: Thursday, April 12, 2018 10:03:18 PM
To: Elam, Jennifer; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: HCP Young Adult Genetics Data Released on dbGaP!!



Just curious...is there an easy way to identify manuscripts already published 
using the HCP-YA genetics data? I found it tough to search in PubMed (HCP is a 
common acronym), and the HCP website might be incomplete? Specifically, have 
any papers come out yet which went beyond heritability analyses and used a 
structural genetics approach (maybe relating to brain structure/connectivity)?
Many Thanks for any pointers you can provide.
Cheers,
Jenifer



From: 
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Elam, Jennifer <e...@wustl.edu<mailto:e...@wustl.edu>>
Sent: Friday, March 2, 2018 2:45:10 PM
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>; 
hcp-annou...@humanconnectome.org<mailto:hcp-annou...@humanconnectome.org>
Subject: [HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!



News from the Human Connectome Project (HCP)

March 2, 2018

The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce 
the release of all SNP Genotypes collected for HCP-Young Adult (HCP-YA) 
subjects on dbGaP:



Mapping the Human Connectome - Structure, Function, and Heritability: Healthy 
Young Adults (Age 22-35 Years) Including Twins and their Non-Twin Siblings
dbGaP Study Accession: phs001364.v1.p1

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_projects_gap_cgi-2Dbin_study.cgi-3Fstudy-5Fid-3Dphs001364.v1.p1=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=1krCazzqwwoiPwmyKujuyzk7O0lrio34VpkumdS1qYg=cdfWp3LrMcNFnrZ4tfCAtctlDvxd8PdAcFiBSmHab84=>

The dbGaP data comprises array and imputed genotyping and a limited number of 
phenotypic variables (self reported sex, age, twin status, and family IDs) 
collected for 1142 of our 1206 released HCP-

Re: [HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!

[Elam, Jennifer]

Hi Jenifer,

I would use the search string: MH091657 OR "Human Connectome Project" to search 
PubMed for manuscripts that have correctly cited the WU-Minn-Oxford HCP grant 
(over 500 to date!).


I am not aware of papers that fit your criteria, but Tom Nichols (CC'd) would 
know what's out there (and likely what's in the pipeline) from some of the 
community.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Juranek, Jenifer <jenifer.jura...@uth.tmc.edu>
Sent: Thursday, April 12, 2018 10:03:18 PM
To: Elam, Jennifer; hcp-users@humanconnectome.org
Subject: Re: HCP Young Adult Genetics Data Released on dbGaP!!

Just curious...is there an easy way to identify manuscripts already published 
using the HCP-YA genetics data? I found it tough to search in PubMed (HCP is a 
common acronym), and the HCP website might be incomplete? Specifically, have 
any papers come out yet which went beyond heritability analyses and used a 
structural genetics approach (maybe relating to brain structure/connectivity)?
Many Thanks for any pointers you can provide.
Cheers,
Jenifer

From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Elam, Jennifer 
<e...@wustl.edu>
Sent: Friday, March 2, 2018 2:45:10 PM
To: hcp-users@humanconnectome.org; hcp-annou...@humanconnectome.org
Subject: [HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!


News from the Human Connectome Project (HCP)
March 2, 2018
The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce 
the release of all SNP Genotypes collected for HCP-Young Adult (HCP-YA) 
subjects on dbGaP:

Mapping the Human Connectome - Structure, Function, and Heritability: Healthy 
Young Adults (Age 22-35 Years) Including Twins and their Non-Twin Siblings
dbGaP Study Accession: phs001364.v1.p1
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_projects_gap_cgi-2Dbin_study.cgi-3Fstudy-5Fid-3Dphs001364.v1.p1=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=1krCazzqwwoiPwmyKujuyzk7O0lrio34VpkumdS1qYg=cdfWp3LrMcNFnrZ4tfCAtctlDvxd8PdAcFiBSmHab84=>
The dbGaP data comprises array and imputed genotyping and a limited number of 
phenotypic variables (self reported sex, age, twin status, and family IDs) 
collected for 1142 of our 1206 released HCP-YA participants, including 149 
pairs of genetically-confirmed monozygotic twins (298 participants) and 94 
pairs of genetically-confirmed dizygotic twins (188 participants). Other open 
and restricted access subject variables are available in 
ConnectomeDB<https://urldefense.proofpoint.com/v2/url?u=https-3A__db.humanconnectome.org=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=1krCazzqwwoiPwmyKujuyzk7O0lrio34VpkumdS1qYg=bWE8uKTKb3gkwGUl37bm2Z4nbDvJ_RutabvREMGoUmY=>.

dbGaP download of the HCP-YA data requires authorized access through a data 
access request initiated after logging into dbGaP with an eRA 
Commons<https://urldefense.proofpoint.com/v2/url?u=https-3A__era.nih.gov_commons-2Daccount-2Dinformation.cfm=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=1krCazzqwwoiPwmyKujuyzk7O0lrio34VpkumdS1qYg=s1S298Jf8bHrEKJWixReCPUs5ympl9TGCVtnag_kiOk=>
 PI account. General instructions for submitting a successful data access 
request<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_projects_gap_cgi-2Dbin_GetPdf.cgi-3Fdocument-5Fname-3DGeneralAAInstructions.pdf=DwMFAw=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=qOVBcC-E3i4BGdjp2AXfXidjspuPk5EgKLbpRj4WEsg=1krCazzqwwoiPwmyKujuyzk7O0lrio34VpkumdS1qYg=NOYjB-AV_ZhDLnJzisHSKO1evGbGXdeekFjQ9c6cbm4=>
 for dbGaP are linked from the blue box on the study page.
You will need to submit as part of the request:

  *   A research statement and a nontechnical summary statement describing your 
planned use of the data.
  *   The name of the institutional signing official who will certify the terms 
of use assurances on behalf of your institution.
  *   A list of all internal investigators at your institution who will share 
access to the data for the proposed research.
  *   A list of external collaborating investigators.
  *   The name of the information technology (IT) Director for your institution.
  *   Local Institutional Review Board (IRB) approval for use.

Once you are logged in and click Create/Begin a New Research Project, on the 
Choose Datasets tab of the Project Request page, un

[HCP-Users] Reprocessed 7T fMRI data released + S1200 updates

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
April 11, 2018
The HCP consortium is pleased to announce the release of fully reprocessed 7T 
fMRI data for 184 HCP-Young Adult (HCP-YA) subjects for download on 
ConnectomeDB. The rerelease corrects the error 
in the 7T preprocessed fMRI data for all subjects and includes other updates, 
plus the addition of multirun ICA FIX-cleaned 7T retinotopy data.
Why was the reprocessing necessary?
In the previously released 7T preprocessed fMRI data (available March-July, 
2017), all 7T fMRI scans with anterior-to-posterior, A->P phase-encoding 
(labeled *_AP) were unwarped using the incorrect direction in the fMRIVolume 
pipeline, causing the voxels in these scans to be spatially misplaced. Since 
the issue occurred in the early stages of preprocessing, we have fully 
reprocessed all the 7T fMRI data which is now available for download on 
ConnectomeDB.

This release includes:

  *   Corrected minimally preprocessed 7T resting state, movie watching task 
and retinotopy task fMRI data
  *   FIX-cleaned 7T retinotopy data (newly available), in addition to 
reprocessed FIX-cleaned 7T resting state and movie-watching data
  *   Per subject 7T imaging parameters, available as a single "quick 
download": 7T MRI Session Summary CSVs (184 
subjects)
 in ConnectomeDB
  *   Behavioral and individual difference measure updates (applied to all HCP 
subjects, including Retest subjects):
 *   Pain intensity raw score and pain interference T-score (from NIH 
Toolbox) added
 *   Cognition composite scores (from NIH Toolbox) added
 *   Words-In-Noise Audition (from NIH Toolbox) version 2 scores added
 *   Bug fixed in NEO Agreeableness scoring (from UPenn CNP battery)
 *   Achenbach Self-report scores are T-scores, not percentile scores as 
originally reported
 *   Clarified descriptions of several measures in the S1200 release Data 
Dictionary available on the HCP wiki

In addition, the 

 HCP S1200 Reference 
Manual
 has been fully updated with new information regarding 7T data collection and 
protocol details and other fixes since the S1200 release.

A manuscript (Benson et al. 2018) presenting results of an analysis of the HCP 
retinotopy data is soon to be released, along with retinotopy analysis data and 
Connectome 
Workbench 
scenes to be released on the Open Science Framework and 
in the BALSA database. When these resources are 
available, we will announce the release on the HCP-Users email forum (sign up 
here).

Along with the release, we also fixed a bug in the Amazon Web Services (AWS) 
access key regeneration function on ConnectomeDB. Let us know if you have any 
issues regenerating your keys.

Other changes are happening behind-the-scenes at the AWS Public Data Sets 
program. These changes should not affect users of the HCP data on AWS, but they 
are delaying our upload of the reprocessed 7T data to our AWS S3 bucket 
(currently only 3T and Retest HCP data are available on S3). Stay tuned for an 
announcement when 7T data is available.

In case you missed it as of March 2, 2018, all SNP Genotypes collected for 
HCP-Young Adult (HCP-YA) subjects have been released on 
dbGaP.

Thanks again for your interest in the HCP and enjoy the data!
Best,
The WU-Minn HCP Consortium


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Fwd: analysing the 7T rsfMRI

[Elam, Jennifer]

Hi Aser,

First off, if you have 7T preprocessed rfMRI data that we previously released, 
do not use it. There was a processing error that we have now fixed and are 
preparing to rerelease the corrected preprocessed data in the next couple of 
weeks.

If you are processing the unprocessed 7T data yourself, we recommend analyzing 
the runs in AP/PA pairs, or using all 4 runs. Advice on demeaning and 
normalizing the timeseries and then concatenating the runs is on the HCP-Users 
FAQ 
wikipage.


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 Laserboy 1122233 

Sent: Monday, March 26, 2018 10:15:39 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Fwd: analysing the 7T rsfMRI

Hello

I am new to the data and apologies if this is a naive question.

All of the data contain or acquired with AP and or PA. If I would like to use 
for example conn to analyse the data can I just analyse rest 1 (PA) or it has 
to be both? If both how can I combine them or proceed ?

Many thanks

Aser


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] FW: asking for one method to combine LR.nii and RL.nii of dMRI or fMRI data of HCP lifespan pilot 1a

[Elam, Jennifer]

We are not planning to have an initial Lifespan data release until sometime in 
the first half of 2019.


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 Glasser, Matthew 

Sent: Thursday, March 22, 2018 10:17:18 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] FW: asking for one method to combine LR.nii and RL.nii of 
dMRI or fMRI data of HCP lifespan pilot 1a

I am not sure on the timetable, but perhaps someone else can comment.

Peace,

Matt.

From: 张辉 >
Date: Thursday, March 22, 2018 at 10:14 AM
To: Matt Glasser >
Subject: Re:Re: [HCP-Users] asking for one method to combine LR.nii and RL.nii 
of dMRI or fMRI data of HCP lifespan pilot 1a

 Dear Matt
   I have been excited to receive your email. Could I inquire the schedule 
time-table for the lifespan data release of preprocessed data?

Extend greeting!

Zhanghui




At 2018-03-22 22:26:16, "Glasser, Matthew" 
> wrote:
Did you try running the HCP Pipelines on the data?  This will handle the 
combination for dMRI.  For fMRI the data can be combined after sICA+FIX cleanup 
after demeaning (and perhaps variance normalizing) it.  Given that you may not 
wish to deal with preprocessing the lifespan pilot data, you might be better 
off exploring your hypothesis in the already preprocessed young adult HCP data 
and waiting for the lifespan data release of preprocessed data.

Peace,

Matt.

From: 
>
 on behalf of 张辉 >
Date: Thursday, March 22, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] asking for one method to combine LR.nii and RL.nii of dMRI 
or fMRI data of HCP lifespan pilot 1a


Dear Sir



I’m a pediatric neurosurgeon from Guangzhou China. For testing my hypothesis 
inspireed by pediatric neurosurgery practice, I attempt to use the data of HCP 
lifespan pilot 1a to expore the function of some brain region. Although I spent 
about several monthes searching the solution for combining LR.nii and RL.nii of 
dMRI or fMRI data, I find I can’t do it. Could you please send me the solution 
you recommend? Thank you very much!





Best regards, and to my





Zhang hui



发送自 Windows 10 版邮件应用



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] 7T resting state data

[Elam, Jennifer]

Hi Janine,

There was a bug in the processing of the 7T functional data we originally 
released, so we have reprocessed the data from all 184 subjects and are 
preparing the data for release, likely by the end of this month.


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 Janine Bijsterbosch 

Sent: Thursday, March 8, 2018 7:14:53 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] 7T resting state data

Hi,

When I try to download the 7T data from connectome DB all the relevant packages 
are greyed out and no links are available for these downloads. Could you let me 
know when the fix-cleaned 7T resting state data will be available for download 
please?

Thanks!

Best wishes,

Janine


-
Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
janine.bijsterbo...@ndcn.ox.ac.uk


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Connectome in a Box program ending: Final orders taken until 3/31/18

[Elam, Jennifer]

Our inventory is down to our last 3 sets of S1200 HCP Young Adult Connectome in 
a Box drives available for ordering through March 31, 2018, the end date for 
the Connectome in a Box program.


Orders for the remaining drives will be taken on a first-come, first-served 
basis at 
https://store.humanconnectome.org.



The full HCP Young Adult dataset will continue to be available through download 
from ConnectomeDB and though our Amazon Web 
Services
 S3 bucket. In future, HCP data and all CCF-distributed data will be released 
via the NIH National Data Archive, which 
also uses AWS for its underlying storage.

If you have any specific questions related to ordering, feel free to contact us 
at ord...@humanconnectome.org.

Best,
The HCP Data Distribution Team


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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

[Elam, Jennifer]

Hi Osama,

We did not ask the participants specifically about whether they were parents, 
but in the Restricted data there is a variable called "Menstrual_Explain" where 
the female participants can give an explanation for why their current cycles 
are irregular in length. About 25 participants cite having a baby recently and 
breastfeeding for this variable, so that could give you a list of mothers. 
However, there is no variable that confirms that a female participant is *not* 
a mother.


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 Glasser, Matthew 

Sent: Monday, March 5, 2018 8:19:33 AM
To: Osama Abdullah; hcp-users@humanconnectome.org
Cc: Nikos Nikiforakis
Subject: Re: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

I don’t know that Gs and Ps were asked about unfortunately.

Peace,

Matt.

From: 
>
 on behalf of Osama Abdullah 
>
Date: Monday, March 5, 2018 at 12:18 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Nikos Nikiforakis >
Subject: [HCP-Users] question about mother vs. non-mothers in the HCP 1200

Dear HCP'ers,

We are trying to compare brain data for female participants who are mothers vs. 
non-mothers. I have access to the restricted data but couldn't find a field 
that specifies if a female participant gave birth or not.

Does this information exists?

As always thanks for your support and guidance.

Osama

Osama Abdullah, Ph.D.
MRI Physicist – Core Technology Platforms
New York University Abu Dhabi

Computational Research Building (A2), MRI Lab
Abu Dhabi, UAE (EDT + 8 hours)
Office: +971-2-628-4990
Cell:+971-56-679-3378

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

[Elam, Jennifer]

Hi Ely,

The PSQI Component scores are already available in ConnectomeDB. We don't have 
plans to release the MMSE component scores.


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 Ely, Benjamin 

Sent: Wednesday, February 28, 2018 6:33:40 PM
To: Burgess, Gregory
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

Hi Greg and co,

What’s the status on the planned release of PSQI component scores? Also, are 
there plans to release the MMSE (aka Mini) component scores?

Thank you!
-Ely

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] HCP Young Adult Genetics Data Released on dbGaP!!

[Elam, Jennifer]

News from the Human Connectome Project (HCP)
March 2, 2018
The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce 
the release of all SNP Genotypes collected for HCP-Young Adult (HCP-YA) 
subjects on dbGaP:

Mapping the Human Connectome - Structure, Function, and Heritability: Healthy 
Young Adults (Age 22-35 Years) Including Twins and their Non-Twin Siblings
dbGaP Study Accession: phs001364.v1.p1
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1
The dbGaP data comprises array and imputed genotyping and a limited number of 
phenotypic variables (self reported sex, age, twin status, and family IDs) 
collected for 1142 of our 1206 released HCP-YA participants, including 149 
pairs of genetically-confirmed monozygotic twins (298 participants) and 94 
pairs of genetically-confirmed dizygotic twins (188 participants). Other open 
and restricted access subject variables are available in 
ConnectomeDB.

dbGaP download of the HCP-YA data requires authorized access through a data 
access request initiated after logging into dbGaP with an eRA 
Commons PI account. 
General instructions for submitting a successful data access 
request
 for dbGaP are linked from the blue box on the study page.
You will need to submit as part of the request:

  *   A research statement and a nontechnical summary statement describing your 
planned use of the data.
  *   The name of the institutional signing official who will certify the terms 
of use assurances on behalf of your institution.
  *   A list of all internal investigators at your institution who will share 
access to the data for the proposed research.
  *   A list of external collaborating investigators.
  *   The name of the information technology (IT) Director for your institution.
  *   Local Institutional Review Board (IRB) approval for use.

Once you are logged in and click Create/Begin a New Research Project, on the 
Choose Datasets tab of the Project Request page, under Primary Disease select 
"Connectome" to find the HCP dataset. Then proceed with your application.

Best,
WU-Minn HCP Consortium

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


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Correct interpretation of NIH battery test 'Words-in-Noise' in HCP subjects

[Elam, Jennifer]

Hi Robert,

Thank you for pointing us to this problem. The HCP Words in Noise score is 
indeed the NIH Toolbox Words in Noise (WIN) Test computed score, rather than 
the Toolbox Hearing Threshold Test that was erroneously used for the 
description in the Data Dictionary. We will fix the data dictionary with the 
upcoming data release of the corrected 7T fMRI data slated to occur within the 
month.


Here's the full description for the Words in Noise measure from the NIH Toolbox 
Interpretation Guide from the 2012 version we used for HCP:


NIH Toolbox Words-in-Noise Test (WIN)Description:
This test measures a person’s ability to recognize single words presented amid 
varying levels of background noise. It measures how much difficulty a person 
might have hearing in a noisy environment. A recorded voice instructs the 
participant to listen to and then repeat words. The task becomes increasingly 
difficult as the background noise gets louder, thus reducing the 
signal-to-noise ratio. The test is recommended for participants ages 6-85 and 
takes approximately six minutes to administer.
Scoring Process: The examiner scores the participant’s responses as correct or 
incorrect, and a total raw score (out of a maximum of 35 points) is calculated 
by the software for each ear. A percent correct is calculated, which is then 
translated into a threshold score for each ear, in decibels of signal-to-noise 
ratio (dB S/N), using a look-up table (see Appendix C). Alternatively, the 
following equation can be used to calculate the S/N score based on the raw 
score, in lieu of the look-up table. For each ear:WIN_Score = 
26-0.8*WIN_NCorrect
Thus, the best score that can be attained (35 correct) for either ear is -2.0 
dB S/N, and the worst score (0correct) is 26.0 dB S/N. Lower scores, therefore, 
are indicative of better performance on this test. In the Toolbox Assessment 
Scores output file, the score for the better ear is provided in the Computed 
Score column.
Interpretation: Assessment of the ability to understand speech in a noisy 
background yields an ecologically valid measure of hearing because a 
substantial portion of communication in the real world occurs in 
less-than-ideal environments. Moreover, speech perception in noise is often 
difficult to predict from pure-tone thresholds or from speech perception in 
quiet settings. The NIH Toolbox version of the Words-in-Noise Test is newly 
released, so the interpretive guidelines provided are preliminary and may need 
further adjustment as future studies are conducted.As noted above, the range of 
possible scores for each ear is -2.0 to 26.0 dB S/N, with lower scores 
indicative of better performance and, conversely, higher scores potentially 
suggestive of hearing difficulties. For score interpretation with ages 13 and 
above, a cutoff of 10 dB S/N is recommended for the Toolbox version of this 
measure. Participants with a score higher than this cutoff should follow up 
with a hearing professional, specifically an otolaryngologist, who would then 
refer to an audiologist as needed. Users should note that the cutoff suggested 
here is slightly higher than other published versions of this test because 
other versions were conducted in quieter environments.

Again, sorry for the oversight. Let me know if you have further questions.

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 Robert Becker 

Sent: Thursday, March 1, 2018 8:41:06 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Correct interpretation of NIH battery test 
'Words-in-Noise' in HCP subjects


Dear all,

we have trouble understanding what the above test actually tests in the context 
of HCP data. Despite its suggestive name, this test is described (in the 
updated HCP Data Dictionary and its previous version), as a pure-tone 
thresholding test that seems to have nothing to do with understanding words 
embedded in noise or any similar scenario.

The description in the Data Dictionary is pretty clear and excludes any such 
interpretation, it is just that the naming seems confusing and also, there 
actually is a NIH toolbox test called '"Words-in-Noise" that does test how 
subjects comprehend one-syllable words.


Can anyone comment on the exact nature of this test and help us out?

Thanks for your help!

Robert

--
Robert Becker, PhD
Universität Zürich
Psychologisches Institut
Binzmühlestrasse 14
8050 Zürich

Tel: +41 44 63 57234
em...@robertbecker.info

___
HCP-Users mailing list

Re: [HCP-Users] Self-regulation data

[Elam, Jennifer]

Hi Aldo,

The delay discounting trial response time data is available by request by 
anyone who has signed the HCP Open Access data access terms. I can send these 
to you off the list.


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 Aldo Rustichini 

Sent: Monday, February 26, 2018 11:32:09 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Self-regulation data

Hi:

I am working with professor Angus MacDonald and Colin DeYoung (Psychology) on 
the Human Connectome data. I am in particular interested in the data on the 
delay discounting task, described as Self-regulation in the Barch et al 
(NeuroImage 2013) survey paper.

I would like to have access, if possible, to the data on response time in the 
task; or to the time stamps for the data in the task, so that I can compute the 
response time. I would like to estimate a Drift Diffusion Model with the data 
(something we have already successfully done with the 
IMAGEN data for a similar task)

As far as I know,  the data are not released yet

Is there any way I can access the data?

Thank you,


--
Aldo Rustichini
Professor of Economics

Department of Economics
University of Minnesota
1925 4th Street South 4-101, Hanson Hall
Minneapolis, MN   55455-0462
tel: 612 625 4816  fax: 612 624 0209

Federal Reserve Bank of Minneapolis
90 Hennepin Avenue
Minneapolis, MN 55401
tel: 612 204 5000

email: rusti...@umn.edu
site: https://sites.google.com/site/aldorustichini/


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] scan order, session day, scan time variables

[Elam, Jennifer]

Hi Csaba,

I believe that information is still only available per subject in the 
{Subject_ID}_3T.csv file in the Structural unprocessed and Structural 
preprocessed packages. Unpacked, the file should appear in the 
{Study_ID}/{Subject_ID}/unprocessed/3T and  {Study_ID}/{Subject_ID}/T1w 
directories.


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 Csaba Orban 

Sent: Wednesday, February 21, 2018 2:05:53 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] scan order, session day, scan time variables

Hi,

I was wondering if it’s now possible to download scan order, session day, and 
scan time variables as part of the bulk csv downloads?

A post from 2016 mentioned that it might become available in the S1200 release.
hhttps://www.mail-archive.com/hcp-users@humanconnectome.org/msg02922.html

Best wishes,

Csaba

~
Csaba Orban, PhD
Postdoctoral Research Fellow
Department of Electrical & Computer Engineering
National University of Singapore





___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Partial correlations ?

[Elam, Jennifer]

Hi David,

The partial correlation netmats for all the different ICA dimensionalities 
should be in the HCP1200 PTN datasets available at 
https://db.humanconnectome.org/data/projects/HCP_1200 in the 
netmats_3T_HCP1200_MSMAll_d*_ts2.tar.gz tarball contained within the datasets 
for the two groups of subjects.

Here's the relevant section of the page, and a link to the 
documentation
 explaining the datasets available:


HCP1200 Parcellation+Timeseries+Netmats (PTN)

Includes Group-ICA "parcellations" at 6 dimensionalities (levels of detail), 
individual subject node timeseries for each dimensionality, individual subject 
and group average full and partial correlation netmats (parcellated 
connectomes), and scripts for running these high-level connectivity analyses. 
See 
Documentation

 1003 Subjects, recon r177 + r227, PTN 
Release
 (13GB)

 812 Subjects, recon r227 only, PTN 
Release
 (10GB)

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 David Hofmann 

Sent: Sunday, February 18, 2018 2:45:33 PM
To: hcp-users
Subject: [HCP-Users] Partial correlations ?

Hi all,

I'm having trouble finding the data with the partial correlations of e.g. the 
300 ROI ICA for each subject. Can someone point me in the right direction here?

Very much appreciated :).

greetings

David

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] hcp preprocessed data in MNI space

[Elam, Jennifer]

Hi Ze,

The cleaned NIFTI data for the 2 resting state sessions are in the Resting 
State fMRI 1 FIX-Denoised (Extended) and Resting State fMRI 2 FIX-Denoised 
(Extended) packages. The cleaned grayordinate data for both sedssions are in 
the Resting State fMRI FIX-Denoised (Compact) package. The original 
rfMRI_REST1_LR.nii.gz file you asked about is the uncleaned preprocessed NIFTI 
data that is part of the Resting State fMRI 1 Preprocessed package, so yes you 
will need to download the one or more of the packages above if you want to work 
with the Fix-cleaned data.


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 Glasser, Matthew 

Sent: Monday, February 19, 2018 1:26:43 PM
To: redhatw; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] hcp preprocessed data in MNI space

That is the uncleaned NIFTI data.  
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_hp2000_clean.nii.gz
 is the cleaned data.

Peace,

Matt.

From: redhatw >
Date: Monday, February 19, 2018 at 1:24 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] hcp preprocessed data in MNI space

Hi Matt,
Thanks for sharing. Does that mean I have to download the data again (the 
extended package)?  what is the file " rfMRI_REST1_LR.nii.gz "?
Best
Ze

On Mon, Feb 19, 2018 at 2:20 PM, Glasser, Matthew 
> wrote:
This is available in the extended packages, however in general it is not 
recommended to compare cortical data across subjects or studies in MNI space or 
to smooth the data in the volume.  The reasons why are covered here:

https://www.biorxiv.org/content/early/2018/01/29/255620

Peace,

Matt.

From: 
>
 on behalf of redhatw >
Date: Monday, February 19, 2018 at 1:11 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] hcp preprocessed data in MNI space

Dear HCPers,
 I'm looking for a way to get the preprocessed rsfMRI data in the MNI 
space. I have only downloaded the preprocessed data, are there any tool to 
generate that or back-project the MSMAll.dtseries.nii into MNI space?
Also, is this file
rfMRI_REST1_LR.nii.gz
already preprocessed?  I noticed that it is in the MNI space.

Thanks
Ze

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[Elam, Jennifer]

Hi Nina,

We expect to release the reprocessed 7T data by the end of March 2018. Sorry 
for the delay, but we are getting close!


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: Nina de Lacy <dela...@u.washington.edu>
Sent: Friday, February 16, 2018 11:37:25 AM
To: Elam, Jennifer
Cc: Glasser, Matthew; Bryan Paton; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume 
data

Hi there:

My apologies if I missed an email saying that this is finished/released, but I 
was wondering if there was an update on the 7T reprocessing?

Thanks
Nina



On Tue, 5 Dec 2017, Elam, Jennifer wrote:

>
> Hi Bryan and all,
>
> We are entering the final steps in the 7T functional reprocessing and expect 
> to have the data for the 184 7T subjects packaged for release on ConnectomeDB 
> by mid-January 2018 as long as we don't
> run into any more issues. The data will be synched to Amazon S3 within a 
> couple weeks of the release. We were hoping to make it for Christmas/New 
> Year's, but it should be soon after.
>
>
> 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<http://www.humanconnectome.org>
>
>
> 
> From: hcp-users-boun...@humanconnectome.org 
> <hcp-users-boun...@humanconnectome.org> on behalf of Glasser, Matthew 
> <glass...@wustl.edu>
> Sent: Monday, December 4, 2017 5:37:18 PM
> To: Bryan Paton; hcp-users@humanconnectome.org
> Subject: Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume 
> data
> Progress continues to be made.  I¹m not clear what all is left to do, but
> perhaps someone closer to the process can comment.
>
> Sorry for the delay,
>
> Matt.
>
> On 12/4/17, 5:31 PM, "hcp-users-boun...@humanconnectome.org on behalf of
> Bryan Paton" <hcp-users-boun...@humanconnectome.org on behalf of
> bryan.pa...@gmail.com> wrote:
>
> >Hi David and HCP team,
> >
> >Sorry to pester but is the 7T data likely to be processed before Xmas?
> >
> >Thanks.
> >
> >Bryan.
> >
> >
> >On 24/10/2017 13:58, David Van Essen wrote:
> >> Bryan et al.
> >>
> >> Apologies for the delay in releasing the reprocessed 7T data. In
> >> brief, it¹s still not done, and it may take another month or more.
> >> As fate would have it, we decided to implement multi-run ICA-FIX
> >> denoising for the 7T retinotopy data, as we are confident that this
> >> will improve the quality of the released data. For reasons I won¹t
> >> belabor, there has been an unexpected string of technical challenges
> >> in getting the modified pipeline to work properly in our HPC
> >> environment, despite ongoing efforts that will remain intensive until
> >> the reprocessing is complete.
> >>
> >> A corollary is that we have also decided not to carry out a partial
> >> 7T data release, as that would tax our limited staffing resources and
> >> further delay the final full release.
> >>
> >> Please bear with us on this.
> >>
> >> David
> >>
> >>> On Oct 23, 2017, at 9:44 PM, Bryan Paton <bryan.pa...@gmail.com>
> >>> wrote:
> >>>
> >>> Hi There,
> >>>
> >>> No doubt the servers are busy working over time but is anyone able
> >>> to give an ETA (approximate or otherwise) of when the 7T volume
> >>> fMRI data might be finished reprocessing? The estimate in July when
> >>> this issue was identified was about 2 months to do the
> >>> re-processing and vetting.
> >>>
> >>> Many thanks.
> >>>
> >>> Bryan.
> >>>
> >>> ___ HCP-Users mailing
> >>> list HCP-Users@humanconnectome.org
> >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >>
> >___
&

Re: [HCP-Users] [SPAM] References about image reconstruction algorithms

[Elam, Jennifer]

Hi Javier,

The only citation describing both the image reconstruction algorithms is the 
HCP 1200 Subjects Reference Manual on pp. 39-40. The original r177 algorithm is 
more fully discussed in the following that you should cite :

Ŭgurbil K, Xu J, Auerbach EJ, Moeller S, Vu A, Duarte-Carvajalino JM, Lenglet 
C, WU X, Schmitter S, Van de Moortele PF, Strupp J, Sapiro G, De Martino F, 
Wang D, Harel N, Garwood M, Chen L, Feinberg DA, Smith SM, Miller KL, 
Sotiropoulos SN, Jbabdi S, Andersson JL, Behrens TEJ, Glasser MF, Van Essen DC, 
Yacoub E (2013). Pushing spatial and temporal resolution for functional and 
diffusion MRI in the Human Connectome 
Project. 
NeuroImage 80: 80-104.


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 Javier Rasero Daparte 

Sent: Wednesday, January 24, 2018 3:46:52 AM
To: hcp-users@humanconnectome.org
Subject: [SPAM] [HCP-Users] References about image reconstruction algorithms

Dear hcp-users,

About the image reconstruction algorithms, apart from the information provided 
in the wiki page, I would like to include in one of my works some references to 
the details of both r177 and 227 algorithms, but so far I have not found 
anything. Do you know any reference I could cite?

Thanks a lot in advance!

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Behavior data

[Elam, Jennifer]

Hi Jodi,

Have you tried the S1200 Reference 
Manual
 Chapter 5 (p.177 and following) on the Behavioral measures details? Also, many 
references are in the Barch et al. 
2013 paper, 
but they should largely be the same as those in the Ref Manual. Let me know if 
there's something specific you can't track down.


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 Gilman, Jodi 

Sent: Friday, February 9, 2018 11:21:19 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Behavior data

Is there a list of references for all of the behavioral measures collected? I 
am trying to track them down but it is a lot of work.  If these were all in one 
place, that would be so amazing…

Thanks,
Jodi

Jodi Gilman, Ph.D.
Assistant Professor, Harvard Medical School
Center for Addiction Medicine
Massachusetts General Hospital
101 Merrimac St.
Boston, MA 02114
Tel.:617-643-7293
Fax:617-643-1998


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Group contrasts for fmri tasks

[Elam, Jennifer]

Hi Dorothy,

Group average Cohen's D activation task fMRI contrast maps are available in the 
1200 Subjects Group Average dataset available on the S1200 HCP Project 
page. We recommend also 
downloading Connectome 
Workbench 
and viewing the data as scenes according to the included PDF tutorial.


We anticipate also making this dataset available soon on 
BALSA as a reference dataset, but it isn't there yet.


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 Dorothy Sincasto 

Sent: Monday, February 5, 2018 1:42:02 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Group contrasts for fmri tasks

Hi

I would like to get the surface contrasts from some fmri tasks, e.g. left hand 
activation on the motor task, preferably group averaged. I looked at BALSA with 
no success, and DB only has some .feat but not individual contrasts between 
conditions and in a surface space.

I would like to use the peaks as localizers for the MEG tasks, is it possible 
to get it anywhere?

Thanks
Dorothy

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] S1200 complete dataset download

[Elam, Jennifer]

Hi Michelle,

I would use the subject filters at the top of the Subject Dashboard to filter 
for only subjects with 3T MR data (here's a link that might work for that 
search 
https://db.humanconnectome.org/app/template/SubjectDashboard.vm?project=HCP_1200=Subjects%20with%203T%20MR%20Session%20Data),
 then use the download CSV options to download the Open access and Restricted 
behavioral data CSVs just for that group.


If needed, you could add filters for different modalities and completeness 
(e.g. number of rfMRI runs, specific tasks, completeness of runs, etc.) to get 
exactly the group of subjects you want to use in your analysis. Adding subject 
filters is demonstrated on pp.24-26 of the S1200 Reference 
Manual.


There is not a way to combine the open access and restricted access behavioral 
data for a subject group into a single csv for download so you do have to do 
that part manually.


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 Michelle Chiu 

Sent: Tuesday, January 30, 2018 4:16:37 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] S1200 complete dataset download

Does anyone know how I can download a complete excel spreadsheet for the 
restricted S1200 dataset (I have restricted access) that includes the columns 
denoting whether 3T MR is available? Right now I seem to only be able to 
download restricted behavioral data and view 3T availability in a separate tab 
on Connectomedb.
I wanted to make sure I'm not missing anything before manually compiling my own 
master excel spreadsheet with the subj list I need (i.e. subjects with 
restricted behavioral data, MR data, gender, etc).

Thanks!

-Michelle

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] missing movement_regressors.txt file

[Elam, Jennifer]

Hi Michelle,

You need to mount to the /s3/HCP_1200 bucket for the full S1200 subject data. 
the /s3/HCP bucket only includes data on subjects released in the 500 subjects 
release (Nov 2014).


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 Michelle Chiu 

Sent: Tuesday, January 30, 2018 2:07:35 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] missing movement_regressors.txt file

I'm trying to run ICA_AROMA on subjects in the HCP through AWS but I'm getting 
the following error back informing me there is no such file or directory (for a 
few subject numbers) for the following:

/s3/hcp/126426/MNINonLinear/Results/tfMRI_GAMBLING_RL/Movement_Regressors.txt

I see on Connectomedb that there is indeed 3T data for the "missing" subjects, 
although these subject folders appear to be missing in the s3/hcp folder I've 
mounted. Please advise, thanks!



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] [SPAM] about the unrestricted data

[Elam, Jennifer]

To clarify the statement "data has been released over the course of the project 
and early data releases had some differences in processing than later 
releases", imaging data released in the Q1, Q1+Q2, and Q3 HCP Data releases 
were processed with an earlier version of the HCP pipelines. For the 500 
Subjects, 900 Subjects, and 1200 Subjects HCP releases, all imaging data 
(including data collected from Q1-Q3 subjects) were processed consistently and 
subject data from these releases can be compared in analyses. As stated in the 
S1200 Release Reference 
Manual<https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf>,
 we recommend that data from the Q1-Q3 data releases not be mixed with data 
from the S500 and later releases.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of Elam, Jennifer 
<e...@wustl.edu>
Sent: Monday, January 29, 2018 4:34:29 PM
To: 罗; hcp-users
Subject: Re: [HCP-Users] [SPAM] about the unrestricted data


Acquisition Q1- Q13 is the quarter the subject's data were collected in the HCP 
(collected 2012-2015). This is important because 1) some of the earlier data 
was reconstructed with a different reconstruction algorithm than data collected 
later, and 2) data has been released over the course of the project and early 
data releases had some differences in processing than later releases.


Sorry for the delay in response, this message ended up in my spam filter, which 
I am currently sorting through.


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<mailto:e...@wustl.edu>
www.humanconnectome.org<http://www.humanconnectome.org/>



From: hcp-users-boun...@humanconnectome.org 
<hcp-users-boun...@humanconnectome.org> on behalf of 罗 <963619...@qq.com>
Sent: Wednesday, January 17, 2018 7:41:06 PM
To: hcp-users
Subject: [SPAM] [HCP-Users] about the unrestricted data

Dear professors
Can I know what does the third column of the unrestricted behavior data 
'Acquisition' 'Q01～Q13' mean?
Thanks very much!

发自我的iPhone

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Pain intensity scores

[Elam, Jennifer]

Hi Ely,

The NIH Toolbox pain intensity raw scores were collected and are in the 
attached spreadsheet (Retest subjects have 2 scores, first is for the original 
visit, second for the retest visit). It is still in our queue to get these into 
ConnectomeDB for open access release.


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 Ely, Benjamin 

Sent: Monday, January 29, 2018 9:20:10 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Pain intensity scores

Dear HCP team,

I’m interested in the NIH Toolbox Pain Intensity measure (PainIntens_RawScore). 
However, the 500 Subject Release data dictionary states that it was “Excluded 
currently due to glitch in the Toolbox data download”, and it doesn’t seem to 
be mentioned in the updated 1200 Subject Release data dictionary. Could you 
please clarify if these scores were correctly recorded? If so, are they still 
planned for release?

Many thanks,
-Ely

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


S1200_TB_Pain_Intensity_Raw.xlsx
Description: S1200_TB_Pain_Intensity_Raw.xlsx