QuNex 1.0.3 release

News
1

Hi,

We are in the process of releasing our probably biggest update to this day. Release notes are attached below. Since this upgrade includes a lot of new things, the chance of some bugs sneaking through our testing process is a bit larger, please let us know if something is not working as it should. QuNex 1.0.0 will be available over the next couple of days, or early next week if there are some unpredicted delays.

Best, Jure

1.0.0 [QIO]:

  • Replacement of run_turnkey with run_recipe, a much more flexible and powerful engine for transparent and reproducible chaining of QuNex commands (https://qunex.readthedocs.io/en/latest/wiki/UsageDocs/RunningQuNexRecipes.html).
  • run_qa, quality assurance (QA) functionality, which you can use to quickly validate raw neuroimaging data and metadata to check if there are discrepancies between acquired sessions or images. The commands generates input-friendly session lists that can be used in commands that follow and user-readable reports of the QA (https://qunex.readthedocs.io/en/latest/api/gmri/run_qa.html).
  • Updated core functions for functional connectivity analyses, enabling flexible extraction of timeseries and computation of seed-based, ROI-based, and global brain connectivity (GBC). Some of Specific improvements are: a) the ability to work with resting state and different types of task-based data, b) the ability to use different functional connectivity measures (r, rho, covariance, cross correlation, inverse covariance, coherence, mutual information and multivariate autoregressive model coefficients), c) a flexible specification of target ROI using different types of input data and masks, and d) the ability to process mulitple session in a single call, compute and store both session specific and group level results (https://qunex.readthedocs.io/en/latest/wiki/UsageDocs/BOLDFunctionalConnectivity.html).
  • The container now includes the recently released version of HCP Pipelines (v5.0.0), which includes a number of new functionalities and improvements (https://github.com/Washington-University/HCPpipelines).
  • Added support for the HCP longitudinal FreeSurfer pipeline (hcp_long_freesurfer and hcp_long_post_freesurfer commands).
  • Support for the HCP TransmitBias pipeline (hcp_transmit_bias_individual). Also added onboading functionalities for imaging data required by this pipeline (B1).
  • hcp_icafix now uses pyfix by default, to use legacy MATLAB fix, add the --hcp_legacy_fix flag to your command call
  • Simplification of the registration and access process.
  • You can now map HCP derivatives (e.g., denoised concatenated REST BOLDs) from HCP folder structure to QuNex with map_hcp_data.
  • Default value for the hcp_prefs_template_res parameter of hcp_pre_freesurfer is now read and set from the imaging data.
  • Made several optimizations that should make QuNex more user friendly (e.g., automatic setting of parameter values from JSON sidecars, more robust logic for automatic setting of parameter values when they are inferred from imaging data …).
  • Fixed some bugs in our data onboarding functions (import_dicom, import_bids, import_hcp).
  • Fixed a bug in the use of IntendedFor BIDS field.
  • You can now specify ROIs using a .roi file that defines ROIs by the center and radius of a sphere.
  • Easier to understand error reports at several locations.
  • Connectome Workbench updated to the latest version.
  • The commercial rights for the container of QuNex 1.0 (QIO) are transferd to a Yale startup called Manifest Technologies, Inc. For any QuNex container v1.0 commercial licensing inquiries please contact qunex@manifesttech.io.
1 Like
2

Hi,

We will be releasing the 1.0.1 that fixes some issues that were found in our latest release. Below is a full list of fixes:

  • Fixed a bug when image loading was not working as it should in some commands of the analytics pipeline.
  • QuNex now supports scenarios where FM-Magnitude is composed of two acquisitions.
  • run_recipe will now error out if unknown commands are provided in the list.
  • Fixed some minor run_recipe bugs.
  • Fixed a bug in create_session_info where the results were sometimes not what was expected.
  • Made a polish pass over the documentation.
  • Added a run_recipe tutorial to the QuNex quickstart (https://qunex.readthedocs.io/en/latest/wiki/Overview/QuickStart.html).
  • Auto setting of the template resolution for HCP Pipelines is now more robust.
  • QuNex will now printout an error if you want to rerun hcp_freesurfer after hcp_post_freesurfer was already completed on the same session. This scenario is not supported and can cause invalid data. You need to cleanup the data and rerun from hcp_pre_freesurfer if you want to do this.

As always, let us know if something does not work as it should. Thanks!

Best, Jure

3

A new small patch (1.0.2) will be released soon (probably tomorrow):

  • Fixed a bug in import_bids when importing SE pairs.
  • Fixed a bug where bold tag (e.g., rest) was not properly converted into a list of bolds when specified as a parameter value.
  • Added some additional error messages for user friendliness.
  • Fixed a qunex_container bug that did not properly pass some parameters to the called QuNex command.
  • By default, QuNex will now leave the raw imaging data archives on import alone (--archive="leave"). Previously, the default behavior was to move the archive into the QuNex study’s archive subolder (--archive="move").
  • Fixed a bug where hcp_echo_te was not correctly prepared for HCP Pipelines.
  • Fixed some MATLAB code so it is now Octave compliant.

Best, Jure

4

A small patch will be released shortly. 1.0.3 contains the following fixes:

  • Fixed a bug in general_extract_glm_volumes that did not detect the CIFTI version properly.
  • Fixed a bug in hcp_fmri_volume that sometimes loaded too many fieldmaps and then errored out.

Best, Jure