Re: [HCP-Users] aws s3 access

[Denis-Alexander Engemann]

Hi Michael,

For what you are describing and what I was trying initially I'm getting
these nasty errors:

A client error (PermanentRedirect) occurred when calling the ListObjects
operation: The bucket you are attempting to access must be addressed using
the specified endpoint. Please send all future requests to this endpoint:
s3.amazonaws.com

You can fix this issue by explicitly providing the correct region location
using the --region argument, the AWS_DEFAULT_REGION environment variable,
or the region variable in the AWS CLI configuration file.  You can get the
bucket's location by running "aws s3api get-bucket-location --bucket
BUCKET".
If you follow these suggestions you receive other errors, etc. not sure if
it is some silly region issue, I'm calling from Europe, Paris.
But then the region restrictions give you "null", there should not be any
issue I suppose.

--Denis

On Wed, Mar 9, 2016 at 11:46 PM, Michael Hileman  wrote:

> Hi Denis,
>
> I'm able to achieve what I think you're after with the following:
>
> I get the bucket contents with a non-recursive ls call -
> aws s3 ls s3://hcp-openaccess --profile USER
>
> Then I'm able to do a recursive listing akin to what you did but with the
> subdirectory -
> aws s3 ls s3://hcp-openaccess/HCP_900 --recursive --human-readable
> --summarize --profile USER
>
> I'm not sure why we can't do a recursive listing of the bucket root. I'll
> have to consult our sysadmin on that one. Are you getting the error "A
> client error (AccessDenied) occurred when calling the ListObjects
> operation: Access Denied"?
>
> Best,
> Michael
>
> 
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
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[HCP-Users] aws s3 access

[Michael Hileman]

Hi Denis,

I'm able to achieve what I think you're after with the following:

I get the bucket contents with a non-recursive ls call -
aws s3 ls s3://hcp-openaccess --profile USER

Then I'm able to do a recursive listing akin to what you did but with the 
subdirectory -
aws s3 ls s3://hcp-openaccess/HCP_900 --recursive --human-readable --summarize 
--profile USER

I'm not sure why we can't do a recursive listing of the bucket root. I'll have 
to consult our sysadmin on that one. Are you getting the error "A client error 
(AccessDenied) occurred when calling the ListObjects operation: Access Denied"?

Best,
Michael


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[HCP-Users] aws s3 access

[Denis-Alexander Engemann]

Dear HCPs,

currently I'm trying to access the HCP data from the command line on Linux.
I configured the access keys based on the console options in the
ConnectomeDB. With other buckets a command like this would work:

aws s3 ls s3://BUCKET-NAME --recursive --human-readable --summarize
--profile USER

Here, BUCKET-NAME is `hcp-openaccess` and USER would be my profile name
with the credentials.

Note that the following works:

aws s3 ls --profile HCP

2015-02-11 20:54:27 hcp-openaccess

2014-07-19 09:22:09 hcp-openaccess-logs

Any thoughts?

Cheers,

Denis

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Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

[Ely, Benjamin]

Oh okay, still using the 500 Subjects Release data and didn’t think to look for 
hidden files. I see it now. Thanks to both of you!

-Ely


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[HCP-Users] behavioral data: unadjusted vs age-adjusted

[Jasmine Joseph]

Hi HCP users,

In the HCP behavioral dataset (WU-Minn) often 2 values are reported for a
parameter: unadjusted and  age-adjusted (ex: Endurance_Unadj and
Endurance_AgeAdj). I looked at the NIH Toolbox but I wasn't able to find
the method for how the age-adjusted value was calculated.

http://www.nihtoolbox.org/WhatAndWhy/Scoring%20Manual/NIH%20Toolbox%20Scoring%20and%20Interpretation%20Manual%209-27-12.pdf

Does anyone happen to know how they calculated the age-adjusted value?

Thanks for all the help!

Jasmine

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Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

[Stephen Smith]

Hi

> On 9 Mar 2016, at 15:24, Harms, Michael  wrote:
> 
> 
> Hi Steve,
> I’m not seeing a file by that name in the HCP FIX processing.

apologies - I was looking at an example folder from when we trained FIX 
that's the hand training output - which wasn't what was asked for here - sorry!

> 
> In the 900 subject release data, there should be files in the 
> rfMRI_REST?_{LR,RL}_hp2000.ica folders called Noise.txt and Signal.txt that 
> contain the classifications.  But those files are created as part of a 
> “PostFix” script, rather than the initial FIX script itself.  And, I don’t 
> think those particular files were created as part of the 500 subject release 
> packages.
> 
> However, if you are using 500 subject release data, you can find the noise 
> components in the rfMRI_REST?_{LR,RL}_hp2000.ica/.fix file (note that it is 
> dot fix, so unfortunately that info is a bit hidden in the 500 subject 
> release data).  The Signal components are then all the other components not 
> specified in the .fix file.
> 
> 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
> 
> 
> 
> On 3/9/16, 2:10 AM, "hcp-users-boun...@humanconnectome.org 
>  on behalf of Stephen Smith" 
>   on behalf of 
> st...@fmrib.ox.ac.uk > wrote:
> 
> Hi - it's the same as in standard FIX usage - the file listing bad components 
> is called hand_labels_noise.txt - inside the ICA output folder.
> Cheers
> 
> 
>> On 9 Mar 2016, at 03:25, Ely, Benjamin > > wrote:
>> Hi all,
>> I’m interested in running some analyses (particularly smoothness 
>> estimations) on the noise components identified by ICA-FIX. I’ve looked 
>> through several subjects’ ICA folders (e.g., 
>> rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/), which contain a number 
>> of output stats and nifti files, but I can’t find an indication of which 
>> components were classified as “good” and “bad”. Is this information 
>> available?
>> Thanks!
>> -Ely
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org 
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> 
> 
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis,  Oxford University FMRIB Centre
> 
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
> st...@fmrib.ox.ac.uk 
> http://www.fmrib.ox.ac.uk/~steve 
> ---
> 
> Stop the cultural destruction of Tibet
> 
> 
> 
> 
> 
> 
> ___
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> 
> 
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare 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.


---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 






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Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

[Harms, Michael]

Hi Steve,
I’m not seeing a file by that name in the HCP FIX processing.


In the 900 subject release data, there should be files in the
rfMRI_REST?_{LR,RL}_hp2000.ica folders called Noise.txt and Signal.txt that contain the classifications.  But those files are created as part of a “PostFix” script, rather than the initial FIX script
 itself.  And, I don’t think those particular files were created as part of the 500 subject release packages.


However, if you are using 500 subject release data, you can find the noise components in the rfMRI_REST?_{LR,RL}_hp2000.ica/.fix file (note that it is dot fix, so unfortunately
 that info is a bit hidden in the 500 subject release data).  The Signal components are then all the other components not specified in the .fix file.


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







On 3/9/16, 2:10 AM, "hcp-users-boun...@humanconnectome.org on behalf of Stephen Smith"  wrote:


Hi - it's the same as in standard FIX usage - the file listing bad components is called hand_labels_noise.txt - inside the ICA output folder.
Cheers





On 9 Mar 2016, at 03:25, Ely, Benjamin  wrote:

Hi all,

I’m interested in running some analyses (particularly smoothness estimations) on the noise components identified by ICA-FIX. I’ve looked through several subjects’ ICA folders (e.g., rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/), which contain a number
 of output stats and nifti files, but I can’t find an indication of which components were classified as “good” and “bad”. Is this information available?

Thanks!
-Ely
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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre


FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve
---


Stop the cultural destruction of Tibet












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 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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Re: [HCP-Users] Cortical parcellations in Connectome Workbench and FreeSurfer

[Slater David]

Great thanks for your helpful reply.

Unfortunately I'm not working with the HCP data exclusively. In addition we 
have our own data which has been pre-processed with the standard FreeSurfer 
-recon-all pipeline. Thus these subjects do not have a 32k or 164k mesh, 
instead they have typical output surfaces from FreeSurfer...

So if I understand correctly I could do the following:

* Use the '"freesurfer_to_fs_LR" script to create 32k and/or 164k mesh surfaces 
for each subject
* The Gordon parcellation would then have a direct correspondence with these 
meshes (no resampling required)
* The FreeSurfer "mri_label2vol" tool could then be used to create subject 
specific parcellation maps

Is this correct? Am I missing something?

Thanks,
David


-Message d'origine-
De : Donna Dierker [mailto:do...@brainvis.wustl.edu] 
Envoyé : 08 March 2016 18:05
À : Slater David
Objet : Re: [HCP-Users] Cortical parcellations in Connectome Workbench and 
FreeSurfer

I hope someone who has actually done something like this answers, but this page 
might be helpful:

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2vol

I'm less familiar with Freesurfer tools, but conceptually:

* The Gordon parcellation is available on 32k mesh (or 164k at least).
* The subject's individual surface is available in both of those meshes.
* The parcellation could be projected to the ribbon between the white and pial 
surfaces (possibly via mri_label2vol).
* It would not be necessary to resample the parcellation onto the native mesh 
to do this.
* The subject's native mesh is also available in one of the HCP-downloadable 
packages.
* There is a way, using -surface-project-unproject, to convert stuff back to 
native mesh, but it's tough to get your head around it, and I'm not sure it's 
the shortest path in this case.

Again, hopefully someone who has done this will reply. :)


On Mar 8, 2016, at 4:14 AM, Slater David  wrote:

> Hi,
>  
> I have a parcellation I would like to work with from the following paper:
>  
> Gordon, E.M., Laumann, T.O., Adeyemo, B., Huckins, J.F., Kelley, W.M., 
> Petersen, S.E., 2014. Generation and Evaluation of a Cortical Area 
> Parcellation from Resting-State Correlations. Cereb. Cortex bhu239-.
> 
>  
> The cortical parcellations are saved in .gii format for both the fs_LR 32k 
> and 164k meshes. My aim is to create a parcellated volume image for each of 
> my subjects in their native space. I know how to do this with Freesurfer 
> tools but I am a little lost with the fs_LR 32k and 164k mesh formats.
>  
> If I had the parcellation in a standard Freesurfer subject space (e.g. 
> fsaverage) I would transform the parcalletion to the subject native space and 
> convert the surface labels to a volume parcellation. This is similar to how 
> the aparc niftii files are generated.
>  
> How can I get a parcellation of the fs_LR 32k or 164k meshes into a subject's 
> native space parcellation? Or alternatively, how can I convert fs_LR 32k or 
> 164k vertex values to the fsaverage surface?
>  
> Thanks,
> David
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> 


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Re: [HCP-Users] "good" vs. "bad" components in ICA-FIX denoised rsfMRI data

[Stephen Smith]

Hi - it's the same as in standard FIX usage - the file listing bad components 
is called hand_labels_noise.txt - inside the ICA output folder.
Cheers


> On 9 Mar 2016, at 03:25, Ely, Benjamin  wrote:
> 
> Hi all,
> 
> I’m interested in running some analyses (particularly smoothness estimations) 
> on the noise components identified by ICA-FIX. I’ve looked through several 
> subjects’ ICA folders (e.g., 
> rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/), which contain a number of 
> output stats and nifti files, but I can’t find an indication of which 
> components were classified as “good” and “bad”. Is this information available?
> 
> Thanks!
> -Ely
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users


---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve
---

Stop the cultural destruction of Tibet






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