Cannot set values in GIFTI data array loaded from file

[ldaumail]

Dear numpy experts,

I am running fmriprep on singularity with a version 3.01 image

and my whole 76 subjects dataset run in parallel are crashing on our HPC and give this error message:

"
Node:
fmriprep_wf.single_subject_109_wf.func_preproc_ses_1_task_restingstate_wf.bold_surf_wf.medial_nans
Working directory: /mnt/data/loic2/work/fmriprep_wf/single_subject_109_wf/func_preproc_ses_1_task_restingstate_wf/bold_surf_wf/_hemi_rh/medial_nans

Node inputs:

in_file = ['/mnt/data/loic2/work/fmriprep_wf/single_subject_109_wf/func_preproc_ses_1_task_restingstate_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii']
subjects_dir =
target_subject = ['fsaverage5']

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1253, in _run_interface
self.config['execution']['stop_on_first_crash'])))
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1128, in _collate_results
for i, nresult, err in nodes:
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 99, in nodelist_runner
result = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 369, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/freesurfer.py", line 328, in _run_interface
newpath=runtime.cwd)
File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/freesurfer.py", line 463, in medial_wall_to_nan
darray.data[medial] = np.nan
ValueError: assignment destination is read-only
"
Would you know how to fix it?
It looks like there was a modification of numpy, isn't it?

Thanks in advance for your help!

[effigies]

This looks like it's related to numpy/numpy#11739, #697, #700, #702.

GIFTI data arrays are being built with base64.b64decode and zlib.decompress, which return bytes objects instead of bytearray, so they're not writable. We'll need to try to figure out a way to create these arrays without doubling memory.

On the other hand, GIFTI darrays are one-per-timestep, so the cost of copying to bytearrays would be time more than memory, so that might be not be too bad.

The quick fix will be to use numpy 1.15.x until we can fix this.