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Fmriprep in singularity issues
gholland@r17n6:~$ singularity run fmriprep-1.1.2.simg /home/gholland/data/bias_task/fmriprep_sourcedata/ /home/gholland/data/bias_task/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt
190129-09:52:30,713 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.1.2:
* BIDS dataset path: /home/gholland/data/bias_task/fmriprep_sourcedata.
* Participant list: ['01'].
* Run identifier: 20190129-095230_7ed2020b-4ab7-4863-a892-829fcabfc493.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 512, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 202, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 365, in init_single_subject_wf
subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant 01 and task <all>. All workflows require BOLD images.
gholland@r15n8:~$ singularity run fmriprep-1.1.4.simg /home/gholland/data/bias_task/fmriprep_sourcedata/ /home/gholland/data/bias_task/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
/usr/local/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
return f(*args, **kwds)
190129-10:12:49,801 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.1.4:
* BIDS dataset path: /home/gholland/data/bias_task/fmriprep_sourcedata.
* Participant list: ['01'].
* Run identifier: 20190129-101249_063fc434-1d31-4062-b7f4-f0db5858fb9f.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 542, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 210, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 377, in init_single_subject_wf
subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant 01 and task <all>. All workflows require BOLD images.
gholland@r15n8:~$ singularity run poldracklab_fmriprep_1.1.8-2018-10-04-8958de85c5c6.img /home/gholland/data/bias_task/fmriprep_sourcedata/ /home/gholland/data/bias_task/derivatives/ participant --participant-label 01 --fs-license-file ~/license.txt
/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
190129-10:13:36,18 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.1.8:
* BIDS dataset path: /home/gholland/data/bias_task/fmriprep_sourcedata.
* Participant list: ['01'].
* Run identifier: 20190129-101336_ed3316f5-9f6c-47bf-823a-5131f9b436c5.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 552, in build_workflow
ignore_aroma_err=opts.ignore_aroma_denoising_errors,
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 210, in init_fmriprep_wf
ignore_aroma_err=ignore_aroma_err)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 377, in init_single_subject_wf
subject_id, task_id if task_id else '<all>'))
Exception: No BOLD images found for participant 01 and task <all>. All workflows require BOLD images.
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