Hi – I’m using Docker to run the latest version of FMRIPREP and I’m encountering an error when it reaches ICA-AROMA.
ValueError: invalid literal for int() with base 10: ‘Mask and image must be the same size’
I’ve tried to run it on a few different subjects and the error seems to be reproducible. I’ve also tried different flags in the FMRIPREP command (e.g., --ignore-aroma-denoising-errors and --low-mem).
My command is below:
docker run -it --rm -v /Volumes/Smith_Group/BIDS_testing_TUBRIC/PARAM_TEST/BIDS_out_all:/data:ro -v /Volumes/Smith_Group/BIDS_testing_TUBRIC/PARAM_TEST/FMRIPREP_new:/out -v /Users/tug87422/Desktop/license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:latest /data /out participant --participant_label 103 --ignore slicetiming --use-aroma --ignore-aroma-denoising-errors --fs-no-reconall --fs-license-file /opt/freesurfer/license.txt --low-mem
The full output is below:
[Node] Error on "fmriprep_wf.single_subject_104_wf.func_preproc_task_rest_run_08_wf.ica_aroma_wf.ica_aroma" (/root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/ica_aroma_wf/ica_aroma)
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
load_entry_point(‘fmriprep==1.0.8’, ‘console_scripts’, ‘fmriprep’)()
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 267, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py”, line 602, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 168, in run
self._clean_queue(jobid, graph, result=result))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py”, line 227, in _clean_queue
raise RuntimeError("".join(result[‘traceback’]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py”, line 68, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 487, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 571, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py”, line 650, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 516, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/interfaces/report_base.py”, line 51, in _run_interface
ReportCapableInterface, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 1023, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py”, line 960, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
ICA_AROMA.py -den nonaggr -i /root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz -meldir /root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/ica_aroma_wf/melodic -mc /root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/ica_aroma_wf/ica_aroma
Standard output:
------------------------------- RUNNING ICA-AROMA -------------------------------
--------------- ‘ICA-based Automatic Removal Of Motion Artifacts’ ---------------
Step 1) MELODIC
- The existing/specified MELODIC directory will be used.
- The MELODIC directory does not contain the required ‘stats’ folder. Mixture modeling on the Z-statistical maps will be run.
Step 2) Automatic classification of the components - registering the spatial maps to MNI
- extracting the CSF & Edge fraction features
Standard error:
Traceback (most recent call last):
File “/opt/ICA-AROMA/ICA_AROMA.py”, line 200, in
edgeFract, csfFract = aromafunc.feature_spatial(fslDir, outDir, scriptDir, melIC_MNI)
File “/opt/ICA-AROMA/ICA_AROMA_functions.py”, line 388, in feature_spatial
‘-V | awk ‘{print $1}’’])))
ValueError: invalid literal for int() with base 10: ‘Mask and image must be the same size’
Return code: 1
Any ideas?
Thanks!
David