Start using FURY v2 to make visual reports

[mattcieslak]

Summary

Fury v2 gets rid of vtk

Additional details

Next steps

It's in the v2 branch, look in the examples

[LuuuXG]

Hello, I am not sure if I should post here. I use WSL Ubuntu 22.04 + Docker to run QSIRecon 1.1.1, but the default parameters cause an error:

Node plot_peaks failed to run on host dc9ab74ea29a.
250906-13:41:43,329 nipype.workflow ERROR: Saving crash info to /data/qsirecon/sub-TAOHC0261/log/20250906-133744_b1e51c92-4aaa-4c27-81fe-f836b7739953/crash-20250906-134143-root-plot_peaks-a255a8f7-e336-412d-ba94-df02bcf4f1ed.txt
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node plot_peaks.

Cmdline:
recon_plot --background_image /data/qsiprep/sub-TAOHC0261/ses-baseline/dwi/sub-TAOHC0261_ses-baseline_acq-DSIb4000_dir-AP_space-ACPC_dwiref.nii.gz --mask_file /data/qsirecon/sub-TAOHC0261/ses-baseline/dwi/sub-TAOHC0261_ses-baseline_acq-DSIb4000_dir-AP_space-ACPC_desc-brain_mask.nii.gz --mif /tmp/work/qsirecon_1_1_wf/sub-TAOHC0261_convert_shore_recons/sub_TAOHC0261_ses_baseline_acq_DSIb4000_dir_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/intensity_norm/sub-TAOHC0261_ses-baseline_acq-DSIb4000_dir-AP_space-ACPC_desc-preproc_dwiHCP_wm_mtnorm.mif --odfs_image odfs_mosaic.png --odf_rois /tmp/work/qsirecon_1_1_wf/sub-TAOHC0261_convert_shore_recons/sub_TAOHC0261_ses_baseline_acq_DSIb4000_dir_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/odf_rois/crossing_rois_trans.nii.gz --peaks_image peaks_mosaic.png

Stdout:
250906-13:41:35,480 nipype.interface INFO: Running in /tmp/work/qsirecon_1_1_wf/sub-TAOHC0261_convert_shore_recons/sub_TAOHC0261_ses_baseline_acq_DSIb4000_dir_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/plot_peaks
250906-13:41:36,999 nipype.workflow INFO: b''
250906-13:41:36,999 nipype.workflow INFO: b''
250906-13:41:37,0 nipype.interface INFO: converting /tmp/work/qsirecon_1_1_wf/sub-TAOHC0261_convert_shore_recons/sub_TAOHC0261_ses_baseline_acq_DSIb4000_dir_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/intensity_norm/sub-TAOHC0261_ses-baseline_acq-DSIb4000_dir-AP_space-ACPC_desc-preproc_dwiHCP_wm_mtnorm.mif to plot ODF/peaks
250906-13:41:37,669 nipype.interface INFO: Starting a virtual framebuffer for FURY
250906-13:41:37,771 nipype.interface INFO: Plotting ODF Peaks images...
250906-13:41:37,817 nipype.interface INFO: Plotting slice indices {'x': [36, 40, 43], 'y': [44, 49, 53], 'z': [39, 43, 46]}
250906-13:41:41,56 nipype.interface WARNING: 'PeakSlicerActor' object is not iterable

Stderr:
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 404, in run
outputs = self.aggregate_outputs(runtime)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 433, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/reports.py", line 306, in _list_outputs
raise Exception(XVFB_ERROR.format(peaks_file.absolute()))
Exception: ODF/Peak Plotting did not produce the expected output: /tmp/work/qsirecon_1_1_wf/sub-TAOHC0261_convert_shore_recons/sub_TAOHC0261_ses-baseline_acq_DSIb4000_dir_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/plot_peaks/peaks_mosaic.png

This could be due to how QSIRecon was run as a container.
If you ran Singularity/Apptainer with --containall, please also use --writable-tmpfs

This seems to be related to FURY?
If I set --skip-odf-reports, another known nipype connection issue occurs: https://neurostars.org/t/qsirecon-cannot-set-the-undefined-plot-reports-attribute-of-a-dsistudiotrackinginputspec-object/30503
. When I use version 1.0.1, ODF reports can be generated normally.