[HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST

[Nicola Toschi]

Hi list,
  

  

  though a processing error I noticed the following strange
  behaviour:
  

  

  1) When i download the complete structural package using the Aspera 
plugin and extract the
  file I am interested in, I get (for example):
  

  

  rwxrwxrwx 1 nicola users 4175821 Nov 27  2015
  100206.R.sphere.MSMAll.native.surf.gii
  

  

  and this file works fine
  

  

  2) When I fetch the same file through CREST/curl, I get a totally
  different file size (no error messages):
  

  

  -rw-r--r--    1 nicola users 213364 Oct 30 19:56
  100206.R.sphere.MSMAll.native.surf.gii
  

  

  and a parse error when I try to use it.
  

  

  Any Idea what I may be doing wrong?
  

  

  Thanks in advance!!!
  

  

  nicola 


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Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

[Harms, Michael]

Hi,
I don’t think the following is necessarily your problem, but know that the 
simple tensor model is not appropriate at high b-values.  You should either
1)  use the “—kurt” or “—kurtdir" flags which will add a “mean kurtosis” or 
“parallel/perpendicular kurtosis” parameters that can account for 
non-exponential decay
or
2) limit the fitting to just the b=1000 shell (+ b=0’s).

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
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: Tuesday, October 31, 2017 at 3:57 PM
To: "Archer,Derek B" 
Cc: "hcp-users@humanconnectome.org" 
Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

That cannot be the command line as not all the parameters are present.  I agree 
that picture looks incorrect.  Does this happen consistently across subjects?  
What subject is this?

Peace,

Matt.

From: "Archer,Derek B" >
Date: Tuesday, October 31, 2017 at 3:06 PM
To: Matt Glasser >
Subject: RE: [HCP-Users] Inaccurate b0 Image from DTIFIT

Hi Matt –

I am only using one line of code, which is:

dtifit –mask=nodif_brain_mask.nii.gz –bvecs=bvecs –bvals=bvals 
–gradnonlin=grad_dev.nii.gz –out=prefix.

This is the exact line of code I run with data from our group, but instead of 
giving bright ventricles it’s dark.  I’ve attached an image of the Human 
Connectome data.

Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687

From: Glasser, Matthew [mailto:glass...@wustl.edu]
Sent: Tuesday, October 31, 2017 3:08 PM
To: Archer,Derek B >; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

Please post the two command lines and some example images.

Peace,

Matt.

From: 
>
 on behalf of "Archer,Derek B" >
Date: Tuesday, October 31, 2017 at 11:56 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Inaccurate b0 Image from DTIFIT

Hello all –

I am working on running DTIFIT on human connectome project diffusion data, but 
when I run the code using the gradnonlin option, the b0 image doesn’t look 
correct.

On a typical b0 image, the ventricles should be bright.  The output on all of 
my subjects gives me dark ventricles.  Is this inaccurate? Does DTIFIT work 
corrected with high b-values?

Thanks!
Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687


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Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

[Glasser, Matthew]

That cannot be the command line as not all the parameters are present.  I agree 
that picture looks incorrect.  Does this happen consistently across subjects?  
What subject is this?

Peace,

Matt.

From: "Archer,Derek B" >
Date: Tuesday, October 31, 2017 at 3:06 PM
To: Matt Glasser >
Subject: RE: [HCP-Users] Inaccurate b0 Image from DTIFIT

Hi Matt –

I am only using one line of code, which is:

dtifit –mask=nodif_brain_mask.nii.gz –bvecs=bvecs –bvals=bvals 
–gradnonlin=grad_dev.nii.gz –out=prefix.

This is the exact line of code I run with data from our group, but instead of 
giving bright ventricles it’s dark.  I’ve attached an image of the Human 
Connectome data.

Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687

From: Glasser, Matthew [mailto:glass...@wustl.edu]
Sent: Tuesday, October 31, 2017 3:08 PM
To: Archer,Derek B >; 
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

Please post the two command lines and some example images.

Peace,

Matt.

From: 
>
 on behalf of "Archer,Derek B" >
Date: Tuesday, October 31, 2017 at 11:56 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Inaccurate b0 Image from DTIFIT

Hello all –

I am working on running DTIFIT on human connectome project diffusion data, but 
when I run the code using the gradnonlin option, the b0 image doesn’t look 
correct.

On a typical b0 image, the ventricles should be bright.  The output on all of 
my subjects gives me dark ventricles.  Is this inaccurate? Does DTIFIT work 
corrected with high b-values?

Thanks!
Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687


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Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

[Glasser, Matthew]

Please post the two command lines and some example images.

Peace,

Matt.

From: 
>
 on behalf of "Archer,Derek B" >
Date: Tuesday, October 31, 2017 at 11:56 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Inaccurate b0 Image from DTIFIT

Hello all –

I am working on running DTIFIT on human connectome project diffusion data, but 
when I run the code using the gradnonlin option, the b0 image doesn’t look 
correct.

On a typical b0 image, the ventricles should be bright.  The output on all of 
my subjects gives me dark ventricles.  Is this inaccurate? Does DTIFIT work 
corrected with high b-values?

Thanks!
Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687


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Re: [HCP-Users] core dump running dMRI pipeline

[Glasser, Matthew]

I recommend posting this on the FSL list, as it suggests a bug with eddy and 
probably that is more likely to be answered on the FSL list.

Peace,

Matt.

From: 
>
 on behalf of bryon mueller >
Date: Tuesday, October 31, 2017 at 11:15 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] core dump running dMRI pipeline

I am getting a core dump while trying to run the HCP dMRI pipeline, using the 
HCP 3.22 release, FSL 5.0.10, a newer card (Tesla P100 compute 12Gb cap 6.0), 
with a RH7 OS. The error I am getting is:

thrust::system_error thrown in CudaVolume::common_assignment_from_newimage_vol 
after resize() with message: function_attributes(): after 
cudaFuncGetAttributes: invalid device function
terminate called after throwing an instance of 'thrust::system::system_error'
  what():  function_attributes(): after cudaFuncGetAttributes: invalid device 
function
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/DiffusionPreprocessing/scripts/run_eddy.sh:
 line 380: 25767 Aborted (core dumped) ${eddy_command}

The last few lines in the .o file shows the call to eddy_cuda and then:
Entering EddyGpuUtils::LoadPredictionMaker

...Allocated GPU # 0...
Mon Oct 30 18:56:24 CDT 2017 - run_eddy.sh - Completed with return value: 134

I have the cuda 7.5 libraries installed and ldd shows eddy_cuda resolving all 
the libraries. Any suggestions?

Thanks,

Bryon

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[HCP-Users] Inaccurate b0 Image from DTIFIT

[Archer,Derek B]

Hello all -

I am working on running DTIFIT on human connectome project diffusion data, but 
when I run the code using the gradnonlin option, the b0 image doesn't look 
correct.

On a typical b0 image, the ventricles should be bright.  The output on all of 
my subjects gives me dark ventricles.  Is this inaccurate? Does DTIFIT work 
corrected with high b-values?

Thanks!
Derek B. Archer
Postdoctoral Research Fellow
Laboratory for Rehabilitation Neuroscience
(812) 259-0687


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[HCP-Users] core dump running dMRI pipeline

[bryon mueller]

I am getting a core dump while trying to run the HCP dMRI pipeline, using
the HCP 3.22 release, FSL 5.0.10, a newer card (Tesla P100 compute 12Gb cap
6.0), with a RH7 OS. The error I am getting is:

thrust::system_error thrown in
CudaVolume::common_assignment_from_newimage_vol after resize() with
message: function_attributes(): after cudaFuncGetAttributes: invalid device
function
terminate called after throwing an instance of
'thrust::system::system_error'
  what():  function_attributes(): after cudaFuncGetAttributes: invalid
device function
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/DiffusionPreprocessing/scripts/run_eddy.sh:
line 380: 25767 Aborted (core dumped) ${eddy_command}

The last few lines in the .o file shows the call to eddy_cuda and then:
Entering EddyGpuUtils::LoadPredictionMaker

...Allocated GPU # 0...
Mon Oct 30 18:56:24 CDT 2017 - run_eddy.sh - Completed with return value:
134

I have the cuda 7.5 libraries installed and ldd shows eddy_cuda resolving
all the libraries. Any suggestions?

Thanks,

Bryon

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Re: [HCP-Users] dtMRI dense connectome

[Glasser, Matthew]

Not at this time, but you can generate one yourself from the bedpostx
results.

Peace,

Matt.

On 10/30/17, 10:35 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Burke Rosen"  wrote:

>Hello,
>
>I¹m sorry if this is silly question but is the MR diffusion tractography
>based dense connectme matrix described in the link below available from
>ConnectomeDB?
>
>https://www.humanconnectome.org/study/hcp-young-adult/project-protocol/dif
>fusion-tractography
>
>Thank you,
>
>Burke Rosen
>
>
>
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