Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[David Van Essen]

Hi Nina (and others),

The HCP 7T reprocessing is now complete (finally! - there were challenges at 
several stages). Now we’re moving on to the packaging process, which is 
conceptually straightforward but is likely to take weeks before it is done and 
vetted.  We anticipate announcing a release sometime in March. 

Best regards,

David

> On Feb 16, 2018, at 11:37 AM, Nina de Lacy <dela...@u.washington.edu> wrote:
> 
> 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
>> 
>> 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
>> >>
>> >___
>> >HCP-Us

Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[Nina de Lacy]

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



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


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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] ETA for reprocessing of 7T preprocessed fMRI volume data

[Elam, Jennifer]

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


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Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[Glasser, Matthew]

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


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Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[Bryan Paton]

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, it’s 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 won’t
> 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 
>> 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
>
___
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Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[Bryan Paton]

Hi David,

Thanks for the reply and the explanation, glad to hear it is coming 
along and sorry for the technical issues.

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, it’s 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 won’t
> 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 
>> 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
>
___
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Re: [HCP-Users] ETA for reprocessing of 7T preprocessed fMRI volume data

[David Van Essen]

Bryan et al.

Apologies for the delay in releasing the reprocessed 7T data. In brief, it’s 
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 won’t 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  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


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