Re: [HCP-Users] Transformation matrices of HCP 500 Subject Release

2015-12-02 Thread Hodge, Michael
Joo-won, We've recently created a "CREST" experiment for each released subject that should give you access to intermediate/non-relased files in the database via REST and for which you know the paths. Here's an example for subject 100307 for one of the files you're interested in: curl -s -k

Re: [HCP-Users] Having problems with installing aspera, upgrade chromium, download data for doing tutorials with workbench....

2015-12-16 Thread Hodge, Michael
Tim and Greg's suggestions are good ones (using Amazon S3 or Aspera via Windows). I believe the Aspera plugin for Linux is still the older NPAPI style plugin, which Chrome no longer supports. The Windows plugin is a PPAPI style plugin which is supported. You might have some success with

Re: [HCP-Users] Is proprietary aspera browser plugin the only way to download the HCP Open data?

2015-11-24 Thread Hodge, Michael
Hi Cherry, Because of the size of the data, it really is recommended to use either the Aspera-based download mechanism via ConnectomeDB, access the data via Amazon S3 (https://wiki.humanconnectome.org/display/PublicData/Connecting+to+Connectome+Data+via+AWS), or via Connectome-in-a-Box

Re: [HCP-Users] Question regarding downloading HCP structural mri data

2016-05-27 Thread Hodge, Michael
From: Hodge, Michael Sent: Tuesday, May 24, 2016 4:30 PM To: 'Josh Gray' <jgray7...@gmail.com>; hcp-users@humanconnectome.org Subject: RE: [HCP-Users] Question regarding downloading HCP structural mri data Hi Josh, I Just wanted to give you an update since this has taken a while.

Re: [HCP-Users] structrual extended package for HCP_900 subjects on aws

2016-05-09 Thread Hodge, Michael
Hi Denis, We’ve had a number of system issues since Friday night stemming from a power outage over the weekend that took out some equipment. Our Aspera server was definitely in a bad state over the weekend, and we were unable to download as of this morning. Some of the issues are still

Re: [HCP-Users] Question regarding downloading HCP structural mri data

2016-05-24 Thread Hodge, Michael
Hi Josh, I Just wanted to give you an update since this has taken a while. We can recreate the problem on our end, but we’re still working on a resolution. The packages are in place on the server, and the database entries that point to them appear to be correct, so we’re not yet sure why

Re: [HCP-Users] Error downloading 7T_REST_Volume_fix dataset

2016-07-05 Thread Hodge, Michael
Hi Parnesh, Thank you for informing us of the problem accessing the 7T Resting State denoised volume data. We’ve found the source of the problem and should have the link working later today. Regards, Mike From: hcp-users-boun...@humanconnectome.org

Re: [HCP-Users] Error downloading 7T_MOVIE_2mm_fix dataset

2016-07-07 Thread Hodge, Michael
gt;http://lists.humanconnectome.org/mailman/listinfo/hcp-users > or, via email, send a message with subject or body 'help' to >hcp-users-requ...@humanconnectome.org > > You can reach the person managing the list at >hcp-users-ow...@humanconnectome.org > > When

Re: [HCP-Users] structrual extended package for HCP_900 subjects on aws

2016-09-08 Thread Hodge, Michael
...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Denis-Alexander Engemann Sent: Thursday, September 8, 2016 12:42 PM To: Hodge, Michael <hod...@wustl.edu>; Jennifer Elam <el...@pcg.wustl.edu>; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] structrual exte

Re: [HCP-Users] (files) listing for file bundles

2016-12-06 Thread Hodge, Michael
, 2016 11:25 AM To: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] (files) listing for file bundles On Tue, 06 Dec 2016, Hodge, Michael wrote: > I've attached unzip -l output for the packages of a couple of subjects. One > has MEG data in addition to the standard 3T data, and the

Re: [HCP-Users] motion parameters

2017-04-21 Thread Hodge, Michael
I don't believe the CREST resources documented on the wiki page have been generated yet for the 1200 release, however the data can be accessed from the session data by iterating over the session data and pipeline output resources. We'll hopefully have the CREST resources generated soon.

Re: [HCP-Users] motion parameters

2017-04-21 Thread Hodge, Michael
- From: hcp-users-boun...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Hodge, Michael Sent: Friday, April 21, 2017 11:32 AM To: Harms, Michael <mha...@wustl.edu>; Ge, Tian <t...@partners.org>; hcp-users@humanconnectome.org Subject: Re: [HCP-U

Re: [HCP-Users] Download aparc+aseg.nii.gz, aseg.stats, lh/rh.aparc.stats of S1200 new subjects

2017-05-09 Thread Hodge, Michael
Hi Jingwei, You’ll want to use a mechanism similar to that discussed in this thread: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg04448.html You can use the XNAT REST protocol to iterate over sessions and resources. The files you’re wanting are structural preprocessing file

Re: [HCP-Users] Test-retest data on AWS?

2017-10-23 Thread Hodge, Michael
Hi Mike, It looks like the CREST resources haven't been generated for the retest project. We'll work on getting those generated, however you can access the files from the pipeline outputs in the retest sessions: curl -u $USERNAME:$PASSWORD -O

Re: [HCP-Users] trouble installing XNAT for QC pipeline

2017-11-10 Thread Hodge, Michael
Hi Maria, Per XNAT’s installation wiki page: XNAT 1.7 was developed and tested exclusively on Tomcat 7. We have had some success running under Tomcat 8, but there are known issues with some combinations of different versions of the

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

2017-11-02 Thread Hodge, Michael
Hi Nicola, What URL are you using to retrieve the file via CREST/curl? When I do: curl -s -k --cookie JSESSIONID=$JSESSIONID

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

2017-11-02 Thread Hodge, Michael
...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Nicola Toschi Sent: Thursday, November 2, 2017 12:02 PM To: Hodge, Michael <hod...@wustl.edu>; hcp-users@humanconnectome.org >> hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Di

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

2017-11-02 Thread Hodge, Michael
contents. Performance should also be a bit better if each call isn’t generating a new session. Regards, Mike From: Hodge, Michael Sent: Thursday, November 2, 2017 12:11 PM To: 'Nicola Toschi' <tos...@med.uniroma2.it>; hcp-users@humanconnectome.org >> hcp-users <hcp-users@humanconnecto

Re: [HCP-Users] volumetric BOLD time series in Native Space?

2018-01-12 Thread Hodge, Michael
From: Glasser, Matthew Sent: Friday, January 12, 2018 5:35 AM To: Osama Abdullah <o...@nyu.edu> Cc: Osama Abdullah <osama.abdul...@utah.edu>; hcp-users@humanconnectome.org; at...@nyu.edu; Hodge, Michael <hod...@wustl.edu>; Brown, Tim <tbbr...@wustl.edu> Subject: Re: [HC

Re: [HCP-Users] mounting temp bucket

2018-07-31 Thread Hodge, Michael
Hi Daniel, I believe we've identified and resolved a bucket-side issue that will hopefully fix the issues you're seeing mounting the temp bucket through s3fs. While we had to use the latest version of s3fs (1.84) to get better diagnostics about the issue, mounting is working for us now using

Re: [HCP-Users] mounting temp bucket

2018-08-14 Thread Hodge, Michael
Hi Michelle, The generation of keys was something we had to do on the bucket. That’s not something you have to do on your end. S3fs requires that the top-level folders have to be represented as objects in the bucket. The lack of those keys was initially preventing mounting. You may want

Re: [HCP-Users] AWS sync error

2018-08-09 Thread Hodge, Michael
Hi Xavier, That message indicates that the access key in your credentials isn't a currently valid access key registered with AWS. I'm thinking that would most likely either be a cut-paste issue or an issue or an issue where the access and secret keys are switched or something similar. One

Re: [HCP-Users] path to bbregister .dat file for REST call

2018-02-28 Thread Hodge, Michael
Hi Olivia, You can use a script similar to this to iterate over all the experiments and preprocessing resources and pull down these files for all subjects: #!/bin/bash # # ITERATE OVER 3T EXPERIMENTS # for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID

Re: [HCP-Users] some scans have _MSMAll_hp2000_clean.dtseries.nii but not MSMSulc cifti or _hp2000_clean.nii.gz ?

2018-10-24 Thread Hodge, Michael
Hi Keith, Yes, I’m seeing this. These were probably lost during the move around of files between buckets. We’ll get the releases re-synced from the data on the WU-side. Thank you for making us aware of this. --Mike From: hcp-users-boun...@humanconnectome.org On Behalf Of Keith Jamison

Re: [HCP-Users] Restricted access

2018-10-09 Thread Hodge, Michael
Hi Jodi, If you look at the "Current Project" selector at the top of the page, there should be another selector next to the project that says "Open Access". If you see that and select one of the restricted access views, you should get a download link for the restricted data. Regards, Mike

Re: [HCP-Users] problems to download the tutorial data set

2019-03-29 Thread Hodge, Michael
Hi Vanessa, I'm hoping this is a transient issue, as there isn't a general problem with the file. It's actually in the same project and directory as the GroupAvg resource that seemed to be downloading successfully, according to your screenshot. The same permissions should apply, and I'm

Re: [HCP-Users] AWS S3 maximum number of attempts (at first attempt)

2019-02-05 Thread Hodge, Michael
: Monday, February 4, 2019 4:46 PM To: Hodge, Michael ; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] AWS S3 maximum number of attempts (at first attempt) Hi Michael, thank you for your reply. I am sorry, I must have copied the wrong log section. I do get the same problem with hcp

Re: [HCP-Users] Downloading Movement Regressor Data for 7T Scans

2019-01-25 Thread Hodge, Michael
Hi Mark, XNAT, upon which ConnectomeDB is based, uses its internal IDs in URLs it returns. Subject ID 100610 isn't guaranteed to be unique across the system. If you use just specify: /data/experiments You'll get a list of all experiments you have access to. One of the columns will be the

Re: [HCP-Users] AWS S3 maximum number of attempts (at first attempt)

2019-02-04 Thread Hodge, Michael
Hi Nicola, I'm able to access the bucket, at the moment, though I'm doing so via the command line. I'm wondering about seeing "hcp-openaccess-trail-temp/" in the log information you sent, though? I do get "Access Denied" if I try to access s3://hcp-openaccess-trail-temp, as that's not one

Re: [HCP-Users] Downloading movement regressors from HYA release

2019-05-30 Thread Hodge, Michael
; hcp-users@humanconnectome.org Cc: Hodge, Michael Subject: Re: [HCP-Users] Downloading movement regressors from HYA release Which specific files (i.e., which runs) is curl not finding for those remaining subjects? Mike Hodge will likely need to investigate further, because I’m able to find

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

2019-06-19 Thread Hodge, Michael
Hi Vanessa, I'm assuming there's either a firewall issue preventing the download or that the browser isn't allowing the plugin to launch. If you right click on Aspera in the system tray (start it up if it's not running), there should be a "Run Diagnostic" link that you can use to check for

Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

2019-06-10 Thread Hodge, Michael
Hi Christina, After discussion with the technician who produced the Connectome in a Box drives, we're thinking what you're seeing could be an issue specific to your copy of the drives. I'll contact you off-list to discuss. Regards, Mike From: hcp-users-boun...@humanconnectome.org On

Re: [HCP-Users] Question on download dMRI.

2019-05-16 Thread Hodge, Michael
Hi Seungyong, There is a command-line Aspera client, but it’s not supported for the HCP data because it would require each user to have account on the Aspera server. However, from the landing page in ConnectomeDB, You’ll see an “Explore Subjects” download. If you select, say the “100