Hi everyone,
I have been running the following command on a HPC system:
fmriprep_1.1.8_withFS bids deriv/Ayshafmriprep1.1.8 participant --participant-label en08a --use-aroma
I have successfully used this command for about 20 other data sets from the same study with no errors. However, I am getting the below error for a couple of data sets (edited just to show the output immediately preceding the error). I have checked the data sets causing the error, and there does not appear to be anything different with them.
I am not sure what is going on, as I couldn’t find anything on FSL’s message board related to a similar error.
Any help would be greatly appreciated.
Thanks in advance,
Aysha
Working directory: /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/ica_aroma
Node inputs:
TR = 1.0
args = <undefined>
compress_report = auto
denoise_type = nonaggr
dim = <undefined>
environ = {}
feat_dir = <undefined>
fnirt_warp_file = <undefined>
in_file = /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz
mask = <undefined>
mat_file = <undefined>
melodic_dir = /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/melodic
motion_parameters = /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/bold_hmc_wf/normalize_motion/motion_params.txt
out_dir = out
out_report = ica_aroma_reportlet.svg
report_mask = /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/bold_mni_trans_wf/mask_mni_tfm/ref_image_valid_corrected_brain_mask_maths_trans.nii.gz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 68, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1038, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 975, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
ICA_AROMA.py -tr 1.000 -den nonaggr -i /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz -meldir /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/melodic -mc /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch/aysham/19172491_8/fmriprep_wf/single_subject_en08a_wf/func_preproc_task_task_run_01_wf/ica_aroma_wf/ica_aroma/out
Standard output:
------------------------------- RUNNING ICA-AROMA -------------------------------
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------
Warning! Please check whether the determined TR (of 1.0s) is correct!
Step 1) MELODIC
- The existing/specified MELODIC directory will be used.
Step 2) Automatic classification of the components
- registering the spatial maps to MNI
- extracting the CSF & Edge fraction features
- extracting the Maximum RP correlation feature
Standard error:
Traceback (most recent call last):
File "/opt/ICA-AROMA/ICA_AROMA.py", line 206, in <module>
maxRPcorr = aromafunc.feature_time_series(melmix, mc)
File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 265, in feature_time_series
nmixrows, nmixcols = mix.shape
ValueError: not enough values to unpack (expected 2, got 1)
Return code: 1