OSError: No command "N4BiasFieldCorrection" found.

[pradhanhitesh]

What happened?

I am running mriqc==24.0.2 on python==3.11.4.

When running the command mriqc /path/to/bids/folder /path/to/output/folder participant, I am getting the error OSError: No command "N4BiasFieldCorrection" found on host jonaslab. Please check that the corresponding package is installed. However, I have installed all necessary dependencies such as AFNI, ANTS and Freesurfer.

What command did you use?

mriqc /path/to/bids/folder /path/to/output/folder participant

What version of the software are you running?

24.0.2

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Node: mriqc_wf.anatMRIQC.synthstrip_wf.pre_n4
Working directory: /media/hitesh/G/Models/Test/work/mriqc_wf/anatMRIQC/synthstrip_wf/2d1ac500ddb38599d0be580e6c4e262170261a96/pre_n4

Node inputs:

args = <undefined>
bias_image = <undefined>
bspline_fitting_distance = <undefined>
bspline_order = <undefined>
convergence_threshold = <undefined>
copy_header = True
dimension = 3
environ = {'NSLOTS': '48'}
histogram_sharpening = <undefined>
input_image = /media/hitesh/G/Models/Test/work/mriqc_wf/anatMRIQC/synthstrip_wf/2d1ac500ddb38599d0be580e6c4e262170261a96/pre_clip/clipped.nii.gz
mask_image = <undefined>
n_iterations = <undefined>
num_threads = 48
output_image = <undefined>
rescale_intensities = True
save_bias = False
shrink_factor = <undefined>
weight_image = <undefined>

Traceback (most recent call last):
  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
    result['result'] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/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 pre_n4.

Cmdline:
	N4BiasFieldCorrection -d 3 --input-image /media/hitesh/G/Models/Test/work/mriqc_wf/anatMRIQC/synthstrip_wf/2d1ac500ddb38599d0be580e6c4e262170261a96/pre_clip/clipped.nii.gz --output clipped_corrected.nii.gz -r
Stdout:

Stderr:

Traceback:
	Traceback (most recent call last):
	  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/media/hitesh/G/Models/Test/mriqc_env/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 756, in _run_interface
	    raise OSError(
	OSError: No command "N4BiasFieldCorrection" found on host jonaslab. Please check that the corresponding package is installed.

Additional information / screenshots

No response

[effigies]

In the same environment that you're calling mriqc, can you call N4BiasFieldCorrection?