NIH Blueprint: The Human Connectome Project

News and Updates

Project News | July 24, 2015

Connectome Workbench Bug fix update v1.1.1 Released

Announcing the release of Workbench v1.1.1, that fixes a few bugs that were found in the recently released Workbench v.1.1.

Updates in v1.1.1:

*New Feature: Copy loaded connectivity row data to a connectivity dense scalar file from group average rs-fMRI dense connectome data loaded through a link from ConnectomeDB (see further instructions below).

*New Command:  -metric-to-volume-mapping command added to map a metric (scalar) file to volume space.

*Scenes now save data by full path name so that files that are named the same, but have a different paths, can be correctly displayed.

*For border files in which names have been modified or created and are invoked by a scene, only border names with a status set to On are displayed when the scene is loaded.

*Averaging connectivity across voxels in a Volume label/ROI now works properly.

 

How to copy/save connectivity row data to a connectivity dense scalar file:

When you have the group average functional connectivity file displayed from ConnectomeDB (as in Scenes 5 & 6 from the WB v1.0 tutorial), go to the Connectivity tab and click the Copy button to the left of the listed Connectivity File link. This creates a *.dscalar file with the particular connectivity map you are displaying.

These files should show up in the Layer tab File dropdowns in the Overlay Toolbox. You can save the files you create with File menu > Save/Manage Files before quitting Workbench, for later use.

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Posted by Jenn Elam @ 1:47 pm

Press Releases,Project News | July 9, 2015

Connectome Workbench v1.1 Released

Screen shot 2015-07-09 at 3.59.29 PMWe are pleased to announce the release of version 1.1 of Connectome Workbench (WB) brain visualization and analysis software.

Learn more about Workbench here.

Get Workbench v1.1 at  http://humanconnectome.org/connectome/get-connectome-workbench.html.

New features in WB v1.1 include:

  • Improved Help Searching
  • Border mode improvements including Border optimize to provide semi-automatic optimization of parcel borders based on single or multi-modal gradients
  • Volume ROI drawing/editing added using “Volume” mode functions
  • Loading and viewing of image files enabled (displayed as underlay in selected Viewing Tab)
  • Improvements to parcellated file behavior and display
  • Palette Settings Improvements:
    • High/low threshold value linking and threshold setting via right click on histogram functions added
    • Thresholding and Palette ranges and step sizes respect range of data
    • Absolute Percentile Palette range and Normalize palette function added
  • Full File names/paths in Layers are displayed via tooltips and copy functions added to Layer construction menu
  • Charting Improvements:
    • Series chart History display options added
    • Toggle display of selection of rows in matrix chart added
  • Identify Brainordinate function (head Icon in Toolbar) added for selecting or highlighting a brainordinate, parcel, or CIFTI row
  • Volume ID symbol may be displayed upon clicking voxels (option in Preferences)
  • Changes to existing command behavior:
    • -cifti-extrema now writes dscalar
    • more error checking in -probtrackx-dot-convert
    • -cifti-replace-structure on label files doesn’t drop unused keys unless asked
    • -metric-fill-holes, -metric-remove-islands use surface area
    • -set-map-names will error if no options to change map names are present
  • New commands and features:
    • -cifti-create-dense-from-template for easier creation of cifti files with matching brainordinates
    • command help format shortened by moving parameters with descriptions to the top, replacing the bare list of parameters
    • -*-stats and -*-weighted-stats
    • equality/boolean operators added in -*-math
    • -cifti-separate can now output label volume for subcortical structures
    • -cifti-convert -*-text for transferring data to/from other tools
    • -cifti-copy-mapping
    • better formatting of command help, logging info, wb_command errors
    • deprecated commands (those that have been replaced with other commands) are available with via: -list-deprecated-commands

WB v1.1 is compatible with the upcoming 2015 HCP Course practical instructions and data (look for this in the next 1-2 weeks!) and the WB v1.0 tutorial and dataset featuring processed HCP 500 Subjects data available to download at http://humanconnectome.org/connectome/get-connectome-workbench.html and on the ConnectomeDB HCP project page. Access to the tutorial data requires ConnectomeDB login and signature of the HCP Open Access Data Use Terms.

To download the WB v1.1 source code from GitHub: follow the link, click releases (near the top of the page), then under v1.1, click the “Source code (zip)” or “Source code (tar.gz)” button .

We encourage you to check out Connectome Workbench v1.1 for visualizing and performing analysis on imaging data from the HCP and elsewhere. Discussion of Connectome Workbench usage, bugs, and features can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe

Press Releases,Project News | April 29, 2015

Release of Improved Group Average Dense Connectome for 500 Subjects R468

Screen shot 2015-04-27 at 4.17.35 PMWe are pleased to announce the release of an improved Group Average Dense Connectome based on resting state fMRI data from 468 subjects that were part of the 500 Subjects Release (the R468 group).

A number of processing pipelines are currently being implemented and refined by the HCP that carry out further analyses at the group level. As of April 2015, with improved analysis methods detailed on the HCP website: Correcting for the rfMRI Mound-and-Moat Effect, we have updated the group-average functional connectivity dataset we are distributing on the 500 Subjects Release R468 group (468 subjects, including many subjects that are related, with complete resting state fMRI data).

The group-average data are available for download through the links on the WU-Minn HCP Project page in ConnectomeDB. One can view the subjects included in this analysis using the “Open group” function on the ConnectomeDB dashboard.

The group-average rfMRI data includes:

  • Group-average functional connectivity matrix (“dense” functional connectome, the grayordinate × grayordinate full correlation matrix), for the R468 group. Because of its large size (33 GB) this dense functional connectome file is released separately from the rest of the group average data.
  • Group-PCA eigenmaps for the R468 group. These can be used as input to group-ICA. They can also be used to generate the dense connectome, but to do this optimally is not trivial, and requires following the procedures outlined in Correcting for the rfMRI Mound-and-Moat Effect.

If you prefer to view the dense connectome file in Connectome Workbench (recommended), you do not need to download it. The data are accessible in Workbench by remote access (requires internet connection and ConnectomeDB login), using the following URL: https://db.humanconnectome.org/spring/cifti-average?resource=HCP_Resources:GroupAvg:HCP_S500_R468_rfMRI_MIGP_d4500ROW_zcorr

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