Node t1_2_mni failed to run

[GalKepler]

Hi, I'm trying to run qsiprep version 0.15.3 and I receive the following error:

Node: qsiprep_wf.single_subject_211_wf.anat_preproc_wf.t1_2_mni Working directory: /work/qsiprep_wf/single_subject_211_wf/anat_preproc_wf/t1_2_mni

Node inputs:

compress_report = auto explicit_masking = True flavor = precise float = True initial_moving_transform = lesion_mask = moving = T1w moving_image = moving_mask = num_threads = 8 orientation = LPS out_report = report.svg reference = T1w reference_image = /usr/local/miniconda/lib/python3.8/site-packages/qsiprep/data/mni_1mm_t1w_lps_brain.nii.gz reference_mask = settings = template = MNI152NLin2009cAsym template_resolution = 1

Traceback (most recent call last): File "/home/groot/.local/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/home/groot/.local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/home/groot/.local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/home/groot/.local/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/home/groot/.local/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 429, in run runtime = self._post_run_hook(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/niworkflows/interfaces/registration.py", line 60, in _post_run_hook return super(RobustMNINormalizationRPT, self)._post_run_hook(runtime) File "/home/groot/.local/lib/python3.8/site-packages/nipype/interfaces/mixins/reporting.py", line 50, in _post_run_hook self._generate_report() File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/niworkflows/interfaces/report_base.py", line 55, in _generate_report mask_nii = threshold_img(fixed_image_nii, 1e-3) File "/home/groot/.local/lib/python3.8/site-packages/nilearn/image/image.py", line 824, in threshold_img img_data = _safe_get_data(img, ensure_finite=True, copy_data=copy) File "/home/groot/.local/lib/python3.8/site-packages/nilearn/_utils/niimg.py", line 51, in _safe_get_data img = copy.deepcopy(img) File "/usr/local/miniconda/lib/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/usr/local/miniconda/lib/python3.8/copy.py", line 270, in _reconstruct state = deepcopy(state, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/usr/local/miniconda/lib/python3.8/copy.py", line 270, in _reconstruct state = deepcopy(state, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/usr/local/miniconda/lib/python3.8/copy.py", line 270, in _reconstruct state = deepcopy(state, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/usr/local/miniconda/lib/python3.8/copy.py", line 161, in deepcopy rv = reductor(4) File "indexed_gzip/indexed_gzip.pyx", line 956, in indexed_gzip.indexed_gzip.IndexedGzipFile.reduce File "indexed_gzip/indexed_gzip.pyx", line 737, in indexed_gzip.indexed_gzip._IndexedGzipFile.export_index AttributeError: '_io.BytesIO' object has no attribute 'mode'

Did anyone encounter something similar and know how to handle it?

Thanks in advance!

[mattcieslak]

are you running this on a system with memory limits? Is it in a docker or singularity container?

[GalKepler]

It's a singularity container, and the execution doesn't reach the memory limit as far as I can tell.

[mattcieslak]

The many threads may be causing memory to run out too. An update to a newer version likely would fix this too