Re: [HCP-Users] Assigning the results of -cifti-correlation to appropriate resting state networks

[Glasser, Matthew]

I think you guys already have the corresponding label file.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson mailto:tsc...@mst.edu>>
Date: Wednesday, April 17, 2019 at 1:10 PM
To: "Jayasekera, Dinal" 
mailto:dinal.jayasek...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Assigning the results of -cifti-correlation to 
appropriate resting state networks

I don't know which parcels are assigned to each network, but if you need to 
know the current order of the parcels, wb_command -file-information will show 
that.

If you have a dlabel file with the networks as labels, you can put that through 
-cifti-parcellate to get each parcel labeled with its majority network, and if 
you want a dlabel file containing the reordering you used for the parcels, you 
can use -cifti-parcel-mapping-to-label.

Tim


On Wed, Apr 17, 2019 at 10:32 AM Jayasekera, Dinal 
mailto:dinal.jayasek...@wustl.edu>> wrote:

Dear all,


I have run a wb_command, specifically -cifti-parcellate, -cifti-reorder and 
-cifti-correlation, on some functional connectivity data to extract and plot an 
adjacency matrix on MATLAB. The matrix that is generated is a 360x360 (360 
parcels x 360 parcels) matrix and I'm trying to figure out how to identify the 
parcels of the matrix that represent each resting state network (at least 5 
RSNs for now).


Does anyone have a file/GUI that can enable me to automatically identify each 
RSN's parcels on MATLAB?


Kind regards,
Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis

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Re: [HCP-Users] Assigning the results of -cifti-correlation to appropriate resting state networks

[Timothy Coalson]

I don't know which parcels are assigned to each network, but if you need to
know the current order of the parcels, wb_command -file-information will
show that.

If you have a dlabel file with the networks as labels, you can put that
through -cifti-parcellate to get each parcel labeled with its majority
network, and if you want a dlabel file containing the reordering you used
for the parcels, you can use -cifti-parcel-mapping-to-label.

Tim


On Wed, Apr 17, 2019 at 10:32 AM Jayasekera, Dinal <
dinal.jayasek...@wustl.edu> wrote:

> Dear all,
>
>
> I have run a wb_command, specifically -cifti-parcellate, -cifti-reorder
> and -cifti-correlation, on some functional connectivity data to extract and
> plot an adjacency matrix on MATLAB. The matrix that is generated is a
> 360x360 (360 parcels x 360 parcels) matrix and I'm trying to figure
> out how to identify the parcels of the matrix that represent each resting
> state network (at least 5 RSNs for now).
>
>
> Does anyone have a file/GUI that can enable me to automatically identify
> each RSN's parcels on MATLAB?
>
>
> Kind regards,
> *Dinal Jayasekera *
>
> PhD Candidate | InSITE Fellow 
> Ammar Hawasli Lab 
> Department of Biomedical Engineering
>  | Washington University in St.
> Louis 
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] Assigning the results of -cifti-correlation to appropriate resting state networks

[Jayasekera, Dinal]

Dear all,


I have run a wb_command, specifically -cifti-parcellate, -cifti-reorder and 
-cifti-correlation, on some functional connectivity data to extract and plot an 
adjacency matrix on MATLAB. The matrix that is generated is a 360x360 (360 
parcels x 360 parcels) matrix and I'm trying to figure out how to identify the 
parcels of the matrix that represent each resting state network (at least 5 
RSNs for now).


Does anyone have a file/GUI that can enable me to automatically identify each 
RSN's parcels on MATLAB?


Kind regards,
Dinal Jayasekera

PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering 
| Washington University in St. Louis

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Re: [HCP-Users] question about making RSFC matrices available

[Curtiss, Sandy]

All,

Tim is correct that our IRB only covers use of the original imaging data, not 
derivative imaging data.  What to do with derivative imaging data is up to a 
person’s own IRB.

That said, if there is any restricted data associated with these data files 
(e.g. age, handedness, race, ethnicity, family structure (see 
https://www.humanconnectome.org/study/hcp-young-adult/document/wu-minn-hcp-consortium-restricted-data-use-terms
 for the full list)), then the data cannot be published using the HCP subject 
IDs.

Sandy


Sandra Curtiss, PhD, PMP
Senior Project Manager, Human Connectome Projects
Washington University in St. Louis
scurt...@wustl.edu




From: Thomas Yeo [mailto:yeoye...@gmail.com]
Sent: Tuesday, April 16, 2019 9:03 PM
To: NEUROSCIENCE tim 
Cc: Glasser, Matthew ; Burgess, Gregory 
; Curtiss, Sandy ; 李婧玮 
; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] question about making RSFC matrices available

I see. Thanks.

Regards,
Thomas

On Tue, Apr 16, 2019 at 6:28 PM Timothy Coalson 
mailto:tsc...@mst.edu>> wrote:
We have done so partly because we haven't needed to put many data files on 
github (it would not be simple for the pipelines to fetch 
data-use-terms-protected files from BALSA, for instance).  He first asked 
whether it was okay to put them on github, and the real answer seems to be "ask 
your own institution, not us".

Tim


On Tue, Apr 16, 2019 at 8:00 PM Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Hi Tim,

I guess we have treated such derivative results similarly and put them behind 
the HCP data use terms.  One easy solution would be to upload the results to 
the BALSA database and add the HCP data use terms.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, April 16, 2019 at 5:11 PM
To: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Cc: "Curtiss, Sandy" mailto:scurt...@wustl.edu>>, 李婧玮 
mailto:allhappylife...@gmail.com>>, Thomas Yeo 
mailto:yeoye...@gmail.com>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] question about making RSFC matrices available

However, he is not sharing the HCP data files themselves, but only results 
obtained from using them.  The data use terms only state that the *original 
data* must be distributed under the same terms.  Derived data appears to only 
be covered by "all relevant rules and regulations imposed by my institution", 
and that paragraph looks like it mainly exists to remind users that the data is 
not considered de-identified.

Tim


On Tue, Apr 16, 2019 at 4:56 PM Burgess, Gregory 
mailto:gburg...@wustl.edu>> wrote:
I believe that the Open Access Data Use terms 
(https://www.humanconnectome.org/study/hcp-young-adult/document/wu-minn-hcp-consortium-open-access-data-use-terms)
 require that anyone receiving the data must have first agreed to the Open 
Access Data Use Terms. If my understanding is correct, that would mean that you 
would need to verify that the recipient has accepted the terms before sharing 
with them. I doubt that would be easy to manage on a public site.

--Greg


Greg Burgess, Ph.D.
Senior Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu


On Apr 16, 2019, at 1:24 PM, Thomas Yeo 
mailto:yeoye...@gmail.com>> wrote:

Hi,

Maybe this question has already been answered before, but we have been working 
on the HCP data and have computed our own derivatives, e.g., FC matrices of 
individual subjects.

Is it ok to share these matrices with accompanying HCP subject IDs on our 
personal github/website? If not, how do you suggest we can share these 
derivatives?

Thanks,
Thomas

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