No space left for MRIQC

1

Anyone familiar with this error? Thanks!

Node: workflow_enumerator.anatMRIQCT1w.segmentation
Working directory: /usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/in_file…data…sub-8511…anat…sub-8511_run-01_T1w.nii.gz/segmentation

Node inputs:

args =
bias_iters =
bias_lowpass =
environ = {‘FSLOUTPUTTYPE’: ‘NIFTI_GZ’}
hyper =
ignore_exception = False
img_type = 1
in_files = [’/usr/local/src/mriqc/work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-8511…anat…sub-8511_run-01_T1w.nii.gz/sstrip_orig_vol/sub-8511_run-01_T1w_conformed_calc.nii.gz’]
init_seg_smooth =
init_transform =
iters_afterbias =
manual_seg =
mixel_smooth =
no_bias =
no_pve =
number_classes =
other_priors =
out_basename = segment
output_biascorrected =
output_biasfield =
output_type = NIFTI_GZ
probability_maps =
segment_iters =
segments = True
terminal_output =
use_priors =
verbose =

OSError: [Errno 28] No space left on device

During handling of the above exception, another exception occurred:

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 498, in run
self, report_type=‘postexec’, is_mapnode=isinstance(self, MapNode))
File “/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/utils.py”, line 232, in write_report
fp.write(’\n’.join(lines))
OSError: [Errno 28] No space left on device

2

It means you are out of disk space. If you are running MRIQC via docker for Mac/Windows there is a docker setting to specify how much virtual disk space docker has access to.

3

Thanks! found it.
Also do you have any suggestion for memory and CPU setting?

4

As much as you can really - MRIQC will detect what resources you made available to it and try to use them as efficiently as possible. I doubt it will work if you assign less than 4GB of RAM.