QuNex 1.4.3 release

News
1

We are in the process of releasing QuNex 1.4.0, it includes the following:

  • Updated OS in the container to Debian 13 which should resolve some CUDA issues when using the container.

  • Optimized the container so it is significantly smaller.

  • Added support for the hcp_asl longitudinal pipeline.

  • HCP ASL pipeline is now more flexible through a more extensive parametrization.

  • Improved the import_bids functionality to make it more robust and support additional imaging types and annotations.

  • Fixed a bug where run_palm sometimes did not work properly in the container.

  • Fixed a bug where QuNex sometimes did not communicate success/fail of processing correctly.

  • Fixed several smaller issues and bugs which should improve the overall robustness of QuNex.

  • More robust cifti and nifti tail parsing and usage.

  • run_recipe now ouputs nicer overview logs.

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

Best, Jure

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2

Over the next couple of days, we will be releasing a pretty big QuNex patch (1.4.1) that includes the following updates:

  • Added support for some new HCP Pipelines parameter.
  • Improved handling of NIfTI metadata in our nii loading and saving scripts.
  • qunex_container now has interactive mode, you can enter the container interactively by using --interactive flag.
  • Improved the PALM interface (run_palm command).
  • Fixed a bug in join_fidl when working with CIfTI conc files.
  • Fixed a race condition in run_qc that made everything crash when running across a lot of sessions in parallel on some systems.
  • hcp_fmri_volume now support OnScanner distortion correction method.
  • dwi_legacy_gpu now has a parameter call extra_eddy_args that you can use to customize eddy behavior. By default this is set as it was now hard coded: --fwhm=10,0,0,0,0 --ff=10 --nvoxhp=2000 --flm=quadratic --data_is_shelled --repol --cnr_maps.
  • Fixed a bug where AFNI did not work sometimes inside the container.
  • Mapping files for create_session_info now support asterisk patterns when selecting images. For example, the mapping rule rfMRI_*_AP => bold:rest:phenc(AP) will map all images whose name matches the rfMRI_*_AP pattern (e.g., rfMRI_REST1_AP, rfMRI_REST2_AP, rfMRI_SLEEP_AP) to the defined target (bold1:rest, bold2:rest, bold3:rest, with the appropraiate phenc).
  • Added support for import_bids that merges multi echo BOLD data into a single image that is compliant with HCP multi echo processing. Set --merge_multi_echo="yes" to achieve this.

Best, Jure

3

We are in the process of releasing QuNex 1.4.2 which fixes a minor bug in hcp_fmri_volume that currently does not work under some specific configurations when using SE-FMs.

Best, Jure

4

We are in the process of releasing QuNex 1.4.3, which fixes the following bugs:

  • Fixed a bug in longitudinal pipelines were some log contents were overwritten by others.

  • Fixed a bug with the OnScanner distortion correction method in hcp_fmri_volume.

  • Fixed an issue that popped up when run_qc was executed in a massively parallel way.

  • Fixed the CUDA version so it is compatible with the FSL’s new default (11.0).

  • Optimized symlinking subject and session folders for longitudinal commands.

Best, Jure