Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Matthew Brett]

Hi,

On Wed, Sep 19, 2018 at 8:13 PM, Glasser, Matthew  wrote:
> normalise is the custom function, not rms.

I know - I was just hinting that maybe it would be worth dropping the
requirement for the signal toolbox, by using that one-liner.  Or maybe
there are more signal toolbox functions you need?

Cheers,

Matthew
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Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Matthew Brett]

Hi,

On Wed, Sep 19, 2018 at 7:52 PM, Glasser, Matthew  wrote:
> It is a custom function that I already pointed to.

Am I right in thinking that the rms function boils down to:

sqrt(mean(x .* conj(x), d))

where d is the dimension along which you want to operate (defaulting to 1)?

https://uk.mathworks.com/help/signal/ref/rms.html

Cheers,

Matthew
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Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Glasser, Matthew]

normalise is the custom function, not rms.

Matt.

On 9/19/18, 4:10 PM, "Matthew Brett"  wrote:

>Hi,
>
>On Wed, Sep 19, 2018 at 7:52 PM, Glasser, Matthew 
>wrote:
>> It is a custom function that I already pointed to.
>
>Am I right in thinking that the rms function boils down to:
>
>sqrt(mean(x .* conj(x), d))
>
>where d is the dimension along which you want to operate (defaulting to
>1)?
>
>https://uk.mathworks.com/help/signal/ref/rms.html
>
>Cheers,
>
>Matthew



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Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Glasser, Matthew]

Not sure, I think over all of the HCP and related pipelines the signal
toolbox will have to remain a dependency.

Matt.

On 9/19/18, 4:16 PM, "Matthew Brett"  wrote:

>Hi,
>
>On Wed, Sep 19, 2018 at 8:13 PM, Glasser, Matthew 
>wrote:
>> normalise is the custom function, not rms.
>
>I know - I was just hinting that maybe it would be worth dropping the
>requirement for the signal toolbox, by using that one-liner.  Or maybe
>there are more signal toolbox functions you need?
>
>Cheers,
>
>Matthew



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Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Glasser, Matthew]

It is a custom function that I already pointed to.

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Wednesday, September 19, 2018 at 3:27 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Andrew Poppe mailto:poppe...@gmail.com>>, 
"hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] MATLAB libraries in Resting State Stats script

'rms' appears to be part of the signal toolbox.  'normalize' seems to be a 
built-in matlab function, but I have no idea about 'normalise'.

Tim


On Wed, Sep 19, 2018 at 11:15 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
I believe rms is a matlab provided function.  The custom functions are in here: 
https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Andrew Poppe mailto:poppe...@gmail.com>>
Date: Wednesday, September 19, 2018 at 11:57 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MATLAB libraries in Resting State Stats script

Hello all,

I've been working with the resting state stats batch script, and it seems to be 
running correctly on our data. I have it set to use the compiled "MCR" version 
of the RestingStateStats matlab script.

However, I'd like to make a couple modifications to that script, most notably 
to save out some data files that are not currently set to save to file. When I 
modify the matlab version of the script and then set the shell script to use 
normal matlab instead of MCR, I get errors that functions normalise and rms are 
not defined.

I was wondering if anyone knows where these functions are defined (or what 
library path I'd need to add in the matlab script). I'm hesitant to simply 
write my own versions of those functions since I don't want to assume I know 
exactly how they're normalizing/computing root mean square.

Any help would be appreciated.

Thanks,

Andrew Poppe, Ph.D.
Postdoctoral Researcher
Olin Neuropsychiatry Research Center
Institute of Living
Hartford Hospital

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Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Timothy Coalson]

'rms' appears to be part of the signal toolbox.  'normalize' seems to be a
built-in matlab function, but I have no idea about 'normalise'.

Tim


On Wed, Sep 19, 2018 at 11:15 AM, Glasser, Matthew 
wrote:

> I believe rms is a matlab provided function.  The custom functions are in
> here: https://github.com/Washington-University/HCPpipelines/tree/master/
> global/matlab
>
> Matt.
>
> From:  on behalf of Andrew Poppe <
> poppe...@gmail.com>
> Date: Wednesday, September 19, 2018 at 11:57 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] MATLAB libraries in Resting State Stats script
>
> Hello all,
>
> I've been working with the resting state stats batch script, and it seems
> to be running correctly on our data. I have it set to use the compiled
> "MCR" version of the RestingStateStats matlab script.
>
> However, I'd like to make a couple modifications to that script, most
> notably to save out some data files that are not currently set to save to
> file. When I modify the matlab version of the script and then set the shell
> script to use normal matlab instead of MCR, I get errors that functions
> normalise and rms are not defined.
>
> I was wondering if anyone knows where these functions are defined (or what
> library path I'd need to add in the matlab script). I'm hesitant to simply
> write my own versions of those functions since I don't want to assume I
> know exactly how they're normalizing/computing root mean square.
>
> Any help would be appreciated.
>
> Thanks,
>
> Andrew Poppe, Ph.D.
> Postdoctoral Researcher
> Olin Neuropsychiatry Research Center
> Institute of Living
> Hartford Hospital
>
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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.
>
> ___
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Re: [HCP-Users] FIX denoised 3T task data release?

[Glasser, Matthew]

We do plan to release denoised 3T task data, but I don¹t have a time-table
on that.

We didn¹t specifically make a 59k version of the parcellation, but that is
easy to create with wb_command -cifti-resample and the appropriate spheres
+ vertex area maps.

Matt.

On 9/19/18, 2:08 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Shankar Tumati"  wrote:

>Hello,
>
>We were implementing the hcp_fix_multi_run script on the HCP 3T task
>data. Although the script is running, it is resource intensive.
>It seemed from a previous thread that FIX was implemented on the task
>data:
>https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06605.html
>
>I was wondering if HCP plans to release fix denoised task data soon?
>
>Also, Is the MMP atlas available in 59k space?
>
>Thank you
>
>Shankar Tumati
>
>Mind, Brain Imaging and Neuroethics lab
>University of Ottawa
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[HCP-Users] FIX denoised 3T task data release?

[Shankar Tumati]

Hello,

We were implementing the hcp_fix_multi_run script on the HCP 3T task data. 
Although the script is running, it is resource intensive. 
It seemed from a previous thread that FIX was implemented on the task data: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06605.html

I was wondering if HCP plans to release fix denoised task data soon?

Also, Is the MMP atlas available in 59k space?

Thank you

Shankar Tumati

Mind, Brain Imaging and Neuroethics lab
University of Ottawa
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Re: [HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

[Glasser, Matthew]

That number is something that may be useful when on the scanner fiddling with 
the protocols, but is otherwise irrelevant.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Jinxia Yao mailto:yao...@purdue.edu>>
Date: Tuesday, September 18, 2018 at 6:41 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

Dear Mr/Ms,

First of all, let me thanks for your great work in HCP dataset. I am an 
graduate student from Purdue University in Biomedical Engineering department. 
Recently, I got a question about the SNR appears in protocol manual. I found 
all the detailed session scan protocol (e.g. structural, resting-state) has SNR 
equals 1 in it. I wonder what this SNR really means in the protocol and what 
the difference between this one and the one that in the common sense! The 
attachment is a screenshot of one of the protocols.
Thank you very much!

Bests,
Jinxia (Fiona) Yao
Weldon School of Biomedical Engineering
Purdue University, 2022
yao...@purdue.edu


[cid:1D7E3E10-4F01-40D2-B20C-C2FDAD485E94]


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Re: [HCP-Users] An error when running AtlasRegistionToMNI152_FLIRTandFNIRT.sh

[Glasser, Matthew]

You didn’t set all of the required options:

 --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask=

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of 
"outlook_c843878f00767...@outlook.com"
 
mailto:outlook_c843878f00767...@outlook.com>>
Date: Tuesday, September 18, 2018 at 11:55 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] An error when running 
AtlasRegistionToMNI152_FLIRTandFNIRT.sh

Dear HCP experts

Hi, I am Qunjun, A PhD student in China.

I got an error when I ran PreFreeSurfer.sh. It came out when the program 
proceeded to AtlasRegistionToMNI152_FLIRTandFNIRT.sh.
---
START: AtlasRegistration to MNI152
Unrecognised option /
---
I realized that it maybe due to an needless ‘/’ in script. But after searching 
the script, I still have no idea about this problem.

Anyway, I found a log text in /MNINonLinear/ and  I think it would be helpful 
to fix the problem so I placed it in attachment.

Looking forward to your reply
Best wishes
Qunjun
发送自 Windows 10 版邮件应用


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[HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

[Jinxia Yao]

Dear Mr/Ms,

First of all, let me thanks for your great work in HCP dataset. I am an 
graduate student from Purdue University in Biomedical Engineering department. 
Recently, I got a question about the SNR appears in protocol manual. I found 
all the detailed session scan protocol (e.g. structural, resting-state) has SNR 
equals 1 in it. I wonder what this SNR really means in the protocol and what 
the difference between this one and the one that in the common sense! The 
attachment is a screenshot of one of the protocols.
Thank you very much!

Bests,
Jinxia (Fiona) Yao
Weldon School of Biomedical Engineering
Purdue University, 2022
yao...@purdue.edu


[cid:1D7E3E10-4F01-40D2-B20C-C2FDAD485E94]


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[HCP-Users] An error when running AtlasRegistionToMNI152_FLIRTandFNIRT.sh

[outlook_c843878f00767...@outlook.com]

Dear HCP experts

Hi, I am Qunjun, A PhD student in China.

I got an error when I ran PreFreeSurfer.sh. It came out when the program 
proceeded to AtlasRegistionToMNI152_FLIRTandFNIRT.sh.
---
START: AtlasRegistration to MNI152
Unrecognised option /
---
I realized that it maybe due to an needless ‘/’ in script. But after searching 
the script, I still have no idea about this problem.

Anyway, I found a log text in /MNINonLinear/ and  I think it would be helpful 
to fix the problem so I placed it in attachment.

Looking forward to your reply
Best wishes
Qunjun
发送自 Windows 10 版邮件应用


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/mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh
 --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear 
--t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc 
--t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore 
--t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain 
--t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc 
--t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore 
--t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain 
--ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= 
--owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz
 
--oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz
 --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w 
--ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore 
--ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain 
--ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w 
--ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore 
--ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain 
--fnirtconfig=
PWD = /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer
date: Tue Sep 18 23:35:03 DST 2018
 
/mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh
 --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear 
--t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc 
--t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore 
--t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain 
--t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc 
--t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore 
--t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain 
--ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= 
--owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz
 
--oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz
 --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w 
--ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore 
--ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain 
--ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w 
--ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore 
--ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain 
--fnirtconfig=
PWD = /mnt/d/HCPpipelines/HCPpipelines
date: Wed Sep 19 10:37:36 DST 2018
 
/mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh
 --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear 
--t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc 
--t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore 
--t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain 
--t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc 
--t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore 
--t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain 
--ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= 
--owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz
 
--oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz
 --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w 
--ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore 
--ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain 
--ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w 
--ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore 
--ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain
PWD = /mnt/d/HCPpipelines/HCPpipelines
date: Wed Sep 19 10:40:27 DST 2018
 
/mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh
 --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear 
--t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc 

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

[Glasser, Matthew]

I believe rms is a matlab provided function.  The custom functions are in here: 
https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Andrew Poppe mailto:poppe...@gmail.com>>
Date: Wednesday, September 19, 2018 at 11:57 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MATLAB libraries in Resting State Stats script

Hello all,

I've been working with the resting state stats batch script, and it seems to be 
running correctly on our data. I have it set to use the compiled "MCR" version 
of the RestingStateStats matlab script.

However, I'd like to make a couple modifications to that script, most notably 
to save out some data files that are not currently set to save to file. When I 
modify the matlab version of the script and then set the shell script to use 
normal matlab instead of MCR, I get errors that functions normalise and rms are 
not defined.

I was wondering if anyone knows where these functions are defined (or what 
library path I'd need to add in the matlab script). I'm hesitant to simply 
write my own versions of those functions since I don't want to assume I know 
exactly how they're normalizing/computing root mean square.

Any help would be appreciated.

Thanks,

Andrew Poppe, Ph.D.
Postdoctoral Researcher
Olin Neuropsychiatry Research Center
Institute of Living
Hartford Hospital

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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 
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[HCP-Users] MATLAB libraries in Resting State Stats script

[Andrew Poppe]

Hello all,

I've been working with the resting state stats batch script, and it seems
to be running correctly on our data. I have it set to use the compiled
"MCR" version of the RestingStateStats matlab script.

However, I'd like to make a couple modifications to that script, most
notably to save out some data files that are not currently set to save to
file. When I modify the matlab version of the script and then set the shell
script to use normal matlab instead of MCR, I get errors that functions
normalise and rms are not defined.

I was wondering if anyone knows where these functions are defined (or what
library path I'd need to add in the matlab script). I'm hesitant to simply
write my own versions of those functions since I don't want to assume I
know exactly how they're normalizing/computing root mean square.

Any help would be appreciated.

Thanks,

Andrew Poppe, Ph.D.
Postdoctoral Researcher
Olin Neuropsychiatry Research Center
Institute of Living
Hartford Hospital

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Re: [HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

[Rutger Fick]

Hi Matt,

That wasn't it but I solved the problem, thanks for your help :-)

Rutger

On Wed, 19 Sep 2018 at 13:29, Glasser, Matthew  wrote:

> Are you using the temp server instead of the reactivated real server?
>
> Matt.
>
> From:  on behalf of Rutger Fick <
> fick.rut...@gmail.com>
> Date: Wednesday, September 19, 2018 at 6:54 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Can't use boto to download HCP subjects from AWS
> server anymore
>
> Hello,
>
> Until some time ago I have been able to download HCP subjects directly
> from the AWS server using the package "boto", using both my public and
> private AWS key.
>
> However, when do the same now (also after regenerating my AWS credentials)
> I receive the response "S3ResponseError: 403 Forbidden".
>
> Does anybody have an idea on what has changed, or how to solve this?
>
> Thank you,
> Rutger Fick
>
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>
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> Healthcare Information or other information of a sensitive nature. If you
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> 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] Can't use boto to download HCP subjects from AWS server anymore

[Glasser, Matthew]

Are you using the temp server instead of the reactivated real server?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Rutger Fick mailto:fick.rut...@gmail.com>>
Date: Wednesday, September 19, 2018 at 6:54 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Can't use boto to download HCP subjects from AWS server 
anymore

Hello,

Until some time ago I have been able to download HCP subjects directly from the 
AWS server using the package "boto", using both my public and private AWS key.

However, when do the same now (also after regenerating my AWS credentials) I 
receive the response "S3ResponseError: 403 Forbidden".

Does anybody have an idea on what has changed, or how to solve this?

Thank you,
Rutger Fick

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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.

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[HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

[Rutger Fick]

Hello,

Until some time ago I have been able to download HCP subjects directly from
the AWS server using the package "boto", using both my public and private
AWS key.

However, when do the same now (also after regenerating my AWS credentials)
I receive the response "S3ResponseError: 403 Forbidden".

Does anybody have an idea on what has changed, or how to solve this?

Thank you,
Rutger Fick

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