Created
January 29, 2019 10:14
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Fmriprep in singularity issues
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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. |
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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. |
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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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