saveNode doesn't work properly

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Operating system: Linux Ubuntu 18.04.5 LTS
Slicer version: 4.11.20210226-linux-amd64
Expected behavior: saving a nifti file using saveNode
Actual behavior: not saving

Hi all, I have a code written in python which should load some volumes and a transform and use the module brain resample.

It seems to work fine and when I run it using the command:

./Slicer --no-main-window --python-script /home/user/Desktop/test_3D_slicer.py

it outputs a table with standard output and at the end the line: "Resample Image (BRAINS) completed without errors. The problem is that it doesn’t save the new resampled image. I attach part of the code I use below. This is within a for loop where I change all parameters each iteration.

resampledNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')
parameters = {'inputVolume': itemCT, 'referenceVolume': itemMR, 'outputVolume': resampledNode,
              'warpTransform': itemTransform, 'interpolationMode': 'Linear'}

slicer.cli.run(slicer.modules.brainsresample, None, parameters)
slicer.util.saveNode(resampledNode, output_filename)

It seems to run fine except for not saving the new nifti. But if I copy paste each line of my code in the python interactor (CTRL+3) for just one iteration, it saves it and also in the right folder so surely output_filename is defined correctly.

Any ideas why this happens?

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A post was merged into an existing topic: saveNode not working properly