ter, or has physio not been collected for the 7T
> data?
>
> - Anders
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
Jennifer Elam, Ph.D.
Scientific
of the data in Amazon S3. We’ll
send out another announcement when S3 is up to date.
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
that are not
in the main Structural Preprocessed packages. The structural extended packages
are included in the S900 Connectome in a Box, which is available for order now.
Best,
Jenn
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department
Hi Janine,
The task analysis packages are actually available separately for 2mm and
4mm smoothing levels for grayordinates data. The reason the package sizes
have gotten twice as big for S900 subjects is that now both MSM-Sulc and
MSM-All registered versions are included in the packages for each
Yes, the preprocessed "Structural Extended" package for each subject has
the Freesurfer outputs that are intermediates in the HCP preprocessing
pipelines.
More info about the files output from the HCP pipelines that toy ate
unfamiliar worth is available in the HCP Reference Manual for the 900
for preorders.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org
From
Hi John,
Yes, the scores HCP distributes for dexterity (the only scaled scores NIH
Toolbox sends back to us for dexterity) are for the dominant hand.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department
ted-access-overview.html>
). Because HCP is a twin family study we have had to put in extra safeguards
to protect the privacy and anonymity of our subjects.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Depa
been mostly minor and have only
added to the data available (more details to come).
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO
lant,
aneurism clip)
Moderate to Severe Claustrophobia
Hope that helps.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
of all the current information that
might affect your results.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e
tomeDB
dashboard by fMRI reconstruction version (in the Study Completion category).
See Ramifications of Image Reconstruction Version Differences
<https://wiki.humanconnectome.org/x/RQBJB> for more details.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Projec
Hi Joelle and all,
HCP does have running bedpostX on the diffusion data for HCP Subjects on our to
do list, but this data has not been released yet. We are hoping to have this
available to users by late winter/early spring 2016 after we release 7T data.
Best,
Jenn
Jennifer Elam, Ph.D
Hi Angus,
We are furiously working on getting the 900 Subject Release out to users. We
are hoping to get it out by Thanksgiving if everything goes smoothly this
week.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
that are not in
NIFTI/GIFTI/CIFTI format.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
<mailto:el...@pcg.wustl.edu> el...@pcg.wustl.edu
to get two
or more arrests in a 12-month period for alcohol-related offenses without
meeting criteria for alcohol dependence (which would preempt the diagnosis
of DSM-IV alcohol abuse).
Let us know if you need any more information about this.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach
files
(both hemispheres).
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
e data
and release notes as you are doing your analyses because, while we try to catch
everything, a few little glitches get by us in a project the size of HCP.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Depa
RIC
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
<mailto:el...@pcg.wustl.edu> el...@pc
not yet been released in ConnectomeDB
otherwise. The arrangement of the data (directory structure) as distributed is
also useful for running the practicals.
We are fixing the download links to the Data Only archive. I’ll let the list
know when all is fixed.
Thanks,
Jenn
Jennifer
The links for downloading the HCP Course Data Only on the HCP Course website
(http://humanconnectome.org/courses/2015/exploring-the-human-connectome.php)
have now been fixed. The Data Only zip archive should be ~215GB.
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
unlikely that we will.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
tp://grants.nih.gov/grants/guide/rfa-files/RFA-MH-16-750.html
Application Due Date: *January 6, 2016*
Budgets: $12M in FY2016 to fund 12-15 awards (up to $700,000 in direct
costs per year).
*Non-domestic (non-U.S.) Entities (Foreign Institutions) are eligible to
apply.*
--
Jennifer Elam, Ph.D.
O
of the packages, it works (I just tried it) to open both these files in
Workbench and setup the first as an underlay and the second as the overlay:
{Subject_ID}/T1w/{Subject_ID}/mri/T1w_hires.nii.gz
{Subject_ID}/T1w/aparc.a2009s+aseg.nii.gz
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach
verify the MZ/DZ desigations with genetic data, but if we do that it will be
reported in a separate field in DB, called something like Genetic_zygosity.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org
From: hcp-users-boun
have the correct version. If what you see
does not match this, then update Workbench to the version now available at:
http://humanconnectome.org/software/get-connectome-workbench.html
Best,
The Connectome Workbench Development Team and the WU-Minn HCP Consortium
Jennifer Elam, Ph.D
Is it Connectome in a Box data? Which version do you have (when did you get
it)? Or did you download an earlier version of the data from ConnectomeDB, or
not get the task analysis packages?
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University
Files before quitting Workbench, for later use.
Best,
The Workbench Developers and the WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
/100307.aparc.32k_fs_LR.dlabel.nii
and
{SubjectID}/MNINonLinear/fsaverage_LR32k/100307.aparc.a2009s.32k_fs_LR.dlabe
l.nii
Hope that's what you are looking for!
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department
description.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org
From: hcp
, bugs, and features can be posted to the
hcp-users discussion list. Sign up for hcp-users at
http://humanconnectome.org/contact/#subscribe
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department
://db.humanconnectome.org/data/projects/HCP_500#megatrawl and login
when prompted.
Full documentation on the NetmatsMegatrawl release is at
https://db.humanconnectome.org/megatrawl/HCP500_MegaTrawl_April2015.pdf
(requires login).
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach
Consortium Informatics Team
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
mailto:el...@pcg.wustl.edu el
collected 6 dMRI scans for these subjects (the full HCP dMRI protocol, see
Reference Manual for details), with all directions collected.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy
or the HCP wiki . Thanks
again for your patience!
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362
.
Hope to see you in Hawaii!!
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
obtained the coefficients by writing Dr. Wang, so
I would do that. As Mike says, it would be nice if you reported back your
experience to the list after you do this.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
and
Preprocessed filters selected. This package has all the intermediate
FreeSurfer pipeline outputs in it and is 611GB for all 526 subjects with
structural MRI data in the current release.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University
at the start of the
year.
If you or others have suggestions on more topics you'd like to be part of an
HCP course, please let us know as this will help us prioritize based on user
feedback.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University
We are hoping to release full 7T documentation and 7T pipelines along with
some 7T main HCP data in Spring 2015.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660
Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
mailto:el...@pcg.wustl.edu el...@pcg.wustl.edu
http
for U100 mainly because of the
extra effort it would take in the face of the many other HCP priorities.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St
them more specifically.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
inconvenience.
Best,
The WU-Minn HCP Team
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
mailto:el
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
mailto:el...@pcg.wustl.edu el...@pcg.wustl.edu
http
us
more about how you are doing your clustering so that we can give you the
right commands to create the appropriate files?
4) See 1)
Im forwarding the thread to the list so that others there can confirm/add
to the discussion.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator
section header (only applies to the
selected layer). The section below the dropdown allows you to change the
parameters of the selected Palette. See Overlay and Map Settings in
Workbench Help (click ? icon in upper right of Workbench window) for more
info.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach
Drive SW, Suite 225
Los Angeles, CA 90095-7334
310-206-2101 (Office)
310-206-5518 (Fax)
703-307-7692 (Cell)
email: mailto:mica...@ucla.edu mica...@ucla.edu
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department
You can also cross check with the list of files that we distribute in our
HCP preprocessed fMRI packages in the Reference Manual Appendix 3
http://humanconnectome.org/documentation/S500/HCP_S500_Release_Appendix_III
.pdf .
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human
recommend you look at Glasser
http://www.sciencedirect.com/science/article/pii/S1053811913005053 et al.
2013 for more information on the diffusion and functional preprocessing.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School
asked about and will let you know if they come up with
ideas.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el
Hi Bryan,
We have updated the Connectome Workbench v1.0 Tutorial to clarify setting
the variable path in the set up instructions. Thanks for the feedback!
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department
pipeline first on unprocessed data to generate
the full output, or (2) add this package to the Structural Preprocessed
package.
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy
://humanconnectome.org/resources/faq-disease-related-connectome-researc
h.html .
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St
generated on GE/Phillips systems. We recommend
contacting your respective contact person at GE or Phillips to get connected
with other customers who have implemented the pulse sequence and then you
can contact CMRR for image reconstruction code.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach
for that vertex (e.g. a label name)
will also appear in the Info box.
Using wb_command -nifti-information -print-xml you can get the full CIFTI
XML that contains lists of the vertices within each label, which you can
parse however you want.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org
From: hcp-users-boun
on the wiki.
Best,
WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
mailto:el
It has come to our attention that there was a nonfunctional link to the 500
Subjects Release reference manual in the announcement email. Here is the
correct link :
http://humanconnectome.org/documentation/S500/index.html
For those of you attending OHBM in Hamburg this week, set aside a few
detailed info than what comes out of FreeSurfer, you can get
it by working with the individual subjects imaging data, but someone else will
have to give you advice on how best to do that.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University
access data without being
concerned about heritability issues. Investigators must apply for restricted
access http://humanconnectome.org/data/restricted-access/index.html to view
the family structure of subjects in the database.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human
Hi Chris,
Your request has been added to the queue of items to be added to ConnectomeDB.
We will keep you updated on the status of the ticket.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy
hope you are looking forward to the release!
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362
it before May 15,
2014.
Please let us know if you have any questions
(hcp-users@humanconnectome.org). Join the hcp-users list here
http://humanconnectome.org/contact/#subscribe .
We hope you are looking forward to the release!
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D
Hi Matthias,
If you are still interested in looking at a 7T rfMRI HCP publication, we do
have this one from 2011 from HCP investigators at UMinn:
http://dx.doi.org/10.1016/j.neuroimage.2011.05.008
There is much more to come from HCP at 7T, so stay tuned.
Best,
Jenn
Jennifer Elam, Ph.D
The latest version Workbench beta 0.85 release has not yet gone live, but is
set to occur later today, hopefully by 5pm CDT. Look for the announcement,
download the new version and check to see if the problem still occurs.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human
and elsewhere. Discussion
of Connectome Workbench usage, bugs, and features can be posted to the
hcp-users discussion list. Sign up for hcp-users at
http://humanconnectome.org/contact/#subscribe
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome
used in HCP see Barch
http://www.sciencedirect.com/science/article/pii/S1053811913005272 et al.
2013 or the HCP Q3 Reference Manual
http://humanconnectome.org/documentation/Q3/Q3_Release_Reference_Manual.pdf .
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Yes, we use the 2004 version of NEOFFI (5-factor) that is included in the UPenn
Gur battery, due to the Gur battery’s wide use in other studies.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy
data for their analyses for reporting on our grant.
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
://www.emmanuelcaruyer.com/q-space-sampling.php
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
tel:314-362-9387 314-362-9387
of Connectome Workbench usage, bugs, and features can be posted
to the hcp-users discussion list. Sign up for hcp-users at
http://humanconnectome.org/contact/#subscribe
Best,
The WU-Minn HCP Consortium
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University
-compatible) head model available for each subject
scanned using MEG. MEG data collection began this summer, and the first MEG
data release is scheduled for the fall (November).
Best,
Jenn
Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School
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