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

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 pl

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

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 Behal

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

; 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 the

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

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 Unrelat

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

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 abl

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

Sent: 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 wit

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

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 o

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

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] some scans have _MSMAll_hp2000_clean.dtseries.nii but not MSMSulc cifti or _hp2000_clean.nii.gz ?

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 Se

Re: [HCP-Users] Restricted access

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] mounting temp bucket

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 to

Re: [HCP-Users] AWS sync error

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 th

Re: [HCP-Users] mounting temp bucket

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] path to bbregister .dat file for REST call

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 https://db.humanconnectome.org/da

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

html Regards, Mike From: Glasser, Matthew Sent: Friday, January 12, 2018 5:35 AM To: Osama Abdullah Cc: Osama Abdullah ; hcp-users@humanconnectome.org; at...@nyu.edu; Hodge, Michael ; Brown, Tim Subject: Re: [HCP-Users] volumetric BOLD time series in Native Space? Perhaps Mike and Tim coul

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

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 JDK

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

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' ; hcp-users@humanconnectome.org >> hcp-users Subject: RE: [HCP-Users] Discrepancy in fil

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

...@humanconnectome.org [mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Nicola Toschi Sent: Thursday, November 2, 2017 12:02 PM To: Hodge, Michael ; hcp-users@humanconnectome.org >> hcp-users Subject: Re: [HCP-Users] Discrepancy in files downloaded from the web interface w.r.t CREST o

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

Hi Nicola, What URL are you using to retrieve the file via CREST/curl? When I do: curl -s -k --cookie JSESSIONID=$JSESSIONID https://db.humanconnectome.org/data/projects/HCP_1200/subjects/100206/experiments/100206_CREST/resources/100206_CREST/files/MNINonLinear/Native/100206.R.sphere.MSMAll.na

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

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 https://db.humanconnectome.org/data/archive/proje

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

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 o

Re: [HCP-Users] motion parameters

- 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 ; Ge, Tian ; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] motion parameters I don't believe the

Re: [HCP-Users] motion parameters

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. Somet

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

ber 6, 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

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

...@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 ; Jennifer Elam ; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] structrual extended package for HCP_900 subjects on aws Hi there

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

aging the list at >hcp-users-ow...@humanconnectome.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of HCP-Users digest..." > > > Today's Topics: > > 1. Error downloading 7T_REST_Volume_fix datase

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

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 [mailto:hcp-users-boun...@humanconnectom

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

From: Hodge, Michael Sent: Tuesday, May 24, 2016 4:30 PM To: 'Josh Gray' ; 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. We can recreate the prob

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. 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 th

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

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 being

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

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 Fire

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

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] Is proprietary aspera browser plugin the only way to download the HCP Open data?

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 direct