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

2019-06-18 Thread 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


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

2019-06-18 Thread Timothy Coalson 
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 
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
>

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

2019-06-18 Thread DE CASTRO Vanessa 
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


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Re: [HCP-Users] film_gls error pinv() svd()

2019-06-18 Thread Harms, Michael 

Not really.  You could ask on the FSL list.

--
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: Moataz Assem 
Date: Tuesday, June 18, 2019 at 8:00 AM
To: "Glasser, Matthew" , "Harms, Michael" 
, "hcp-users@humanconnectome.org" 

Subject: RE: [HCP-Users] film_gls error pinv() svd()

Nope, Matt, no empty EVs and estimations worked fine for subcortex with the 
exact same design.

Removing ‘--sa --ms=15 --epith=5’ did make it work. Any ideas what would this 
indicate?

Moataz

From: Glasser, Matthew [mailto:glass...@wustl.edu]
Sent: 18 June 2019 02:54
To: Harms, Michael ; Moataz Assem 
; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] film_gls error pinv() svd()

Is there anything weird about your design like empty EVs?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Monday, June 17, 2019 at 12:55 PM
To: Moataz Assem 
mailto:moataz.as...@mrc-cbu.cam.ac.uk>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] film_gls error pinv() svd()


Hmmm.  Assuming the problem is reproducible, I think you’ll have to report 
this, to the FSL list.  To provide additional information, it might be helpful 
to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’ 
flags in the call to ‘film_gls’ (or, perhaps easier, just try running the 
modified film_gls call directly from the command line).  And if that still 
fails, try turning off the autocorrelation estimation entirely with the 
‘--noest' flag.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Moataz Assem 
mailto:moataz.as...@mrc-cbu.cam.ac.uk>>
Date: Monday, June 17, 2019 at 9:32 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] film_gls error pinv() svd()

Hi,

I get the following fsl error related to the beta estimations (while running 
film_gls):

Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,
error: pinv(): svd failed

pinv(): svd failed

This only happens for one run (in one subject) and while estimating the left 
surface (subcortical estimation ran fine). The design matrix doesn’t contain 
any NaNs neither does the timeseries for that hemisphere (also std(timeseries) 
did not give any zeros).

I am wondering if you can suggest other problems to check for?

Thanks

Moataz



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Re: [HCP-Users] film_gls error pinv() svd()

2019-06-18 Thread Moataz Assem 
Nope, Matt, no empty EVs and estimations worked fine for subcortex with the 
exact same design.

Removing ‘--sa --ms=15 --epith=5’ did make it work. Any ideas what would this 
indicate?

Moataz

From: Glasser, Matthew [mailto:glass...@wustl.edu]
Sent: 18 June 2019 02:54
To: Harms, Michael ; Moataz Assem 
; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] film_gls error pinv() svd()

Is there anything weird about your design like empty EVs?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Monday, June 17, 2019 at 12:55 PM
To: Moataz Assem 
mailto:moataz.as...@mrc-cbu.cam.ac.uk>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] film_gls error pinv() svd()


Hmmm.  Assuming the problem is reproducible, I think you’ll have to report 
this, to the FSL list.  To provide additional information, it might be helpful 
to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’ 
flags in the call to ‘film_gls’ (or, perhaps easier, just try running the 
modified film_gls call directly from the command line).  And if that still 
fails, try turning off the autocorrelation estimation entirely with the 
‘--noest' flag.

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: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Moataz Assem 
mailto:moataz.as...@mrc-cbu.cam.ac.uk>>
Date: Monday, June 17, 2019 at 9:32 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] film_gls error pinv() svd()

Hi,

I get the following fsl error related to the beta estimations (while running 
film_gls):

Prewhitening and Computing PEs...
Percentage done:
1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,
error: pinv(): svd failed

pinv(): svd failed

This only happens for one run (in one subject) and while estimating the left 
surface (subcortical estimation ran fine). The design matrix doesn’t contain 
any NaNs neither does the timeseries for that hemisphere (also std(timeseries) 
did not give any zeros).

I am wondering if you can suggest other problems to check for?

Thanks

Moataz



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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.

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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.

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