numpy in fMRIPrep 21.0.0rc0 #2532
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Ah, good catch. Curious why we didn't see it before. Will submit a fix momentarily. |
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Thanks I will re download the container |
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You'll need to use |
Closed
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I re ran 21.0,0rc0 with the same inputs
The data were processed through and the html file was created.
I looked through the logs and saw this:
cat crash-20210919-130513-root-_resample1-18334bb1-9f5b-4c47-a68d-2781a55f2f87.txt
Node: _resample1
Working directory: /tmp/work/fmriprep_wf/single_subject_patensasc0089_wf/func_preproc_ses_1385_task_gbu_run_02_wf/bold_grayords_wf/resample/mapflow/_resample1
Node inputs:
area_metrics = True
area_surfs = <undefined>
args = <undefined>
current_area = /home/fmriprep/.cache/templateflow/tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_desc-vaavg_midthickness.shape.gii
current_sphere = /home/fmriprep/.cache/templateflow/tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_desc-std_sphere.surf.gii
environ = {}
in_file = /tmp/work/fmriprep_wf/single_subject_patensasc0089_wf/func_preproc_ses_1385_task_gbu_run_02_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata1/rh.fsaverage.gii
largest = <undefined>
method = ADAP_BARY_AREA
new_area = /home/fmriprep/.cache/templateflow/tpl-fsLR/tpl-fsLR_hemi-R_den-32k_desc-vaavg_midthickness.shape.gii
new_sphere = /home/fmriprep/.cache/templateflow/tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-R_den-32k_sphere.surf.gii
out_file = space-fsLR_hemi-R_den-91k_bold.gii
roi_metric = <undefined>
valid_roi_out = <undefined>
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 406, in run
version=self.version,
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/workbench/base.py", line 39, in version
return Info.version()
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 1127, in version
clout = CommandLine(
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
wb_command -version
Standard output:
Standard error:
wb_command: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file or directory
Return code: 127
***@***.*** 20210917-162529_f3075109-8311-4e04-b16f-1c43168379c7]$
…________________________________
From: Sanchez, Juan (NYSPI) ***@***.***>
Sent: Monday, September 13, 2021 8:12 PM
To: nipreps/fmriprep ***@***.***>; nipreps/fmriprep ***@***.***>
Cc: Author ***@***.***>
Subject: Re: [nipreps/fmriprep] numpy in fMRIPrep 21.0.0rc0 (#2532)
Thanks so much I will follow up
From: Chris Markiewicz ***@***.***>
Date: Monday, September 13, 2021 at 3:24 PM
To: nipreps/fmriprep ***@***.***>
Cc: Sanchez, Juan (NYSPI) ***@***.***>, Author ***@***.***>
Subject: Re: [nipreps/fmriprep] numpy in fMRIPrep 21.0.0rc0 (#2532)
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
You'll need to use :unstable until we release a 21.0.0rc1.
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Just merged a fix to that. In an hour or so, you should be able to update |
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Yes. You'll need to |
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What version of fMRIPrep are you using?
fMRIPrep 21.0.0rc0
What kind of installation are you using? Containers (Singularity, Docker), or "bare-metal"?
Docker
What is the exact command-line you used?
Have you checked that your inputs are BIDS valid?
YES
Did fMRIPrep generate the visual report for this particular subject? If yes, could you share it?
Can you find some traces of the error reported in the visual report (at the bottom) or in crashfiles?
Are you reusing previously computed results (e.g., FreeSurfer, Anatomical derivatives, work directory of previous run)?
fMRIPrep log
If you have access to the output logged by fMRIPrep, please make sure to attach it as a text file to this issue.
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