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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
292 stars 130 forks source link

Issue with Traits in mriqc nipype #438

Closed hermeckerogg closed 7 years ago

hermeckerogg commented 7 years ago

So I've built and rebuilt everything more than couple of times now and I keep getting this same error regardless of the mriqc or nipype build that I use:

mriqc ABIDEII-SDSU_1_BIDS ABIDEII-SDSU_1_BIDS/Derivatives/mriqctest participant --participant_label sub-28853
/home/Thomas/miniconda2/lib/python2.7/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
2017-03-29 22:13:40,902 root:INFO Running MRIQC-99.99.99 (analysis_levels=[participant], participant_label=['sub-28853'])
        Settings={u'report_dir': u'/mnt/f/ABIDEII/ABIDEII-SDSU_1_BIDS/Derivatives/mriqctest/reports', u'deoblique': False, u'correct_slice_timing': False, u'ants_nthreads': 6, u'despike': False, u'testing': False, u'hmc_fsl': False, u'fft_spikes_detector': False, u'write_graph': False, u'work_dir': u'/mnt/f/ABIDEII/work', u'verbose_reports': False, u'n_procs': 1, u'bids_dir': '/mnt/f/ABIDEII/ABIDEII-SDSU_1_BIDS', u'hmc_afni': True, u'float32': False, u'output_dir': '/mnt/f/ABIDEII/ABIDEII-SDSU_1_BIDS/Derivatives/mriqctest'}
participant labels  [u'^28853$']
2017-03-29 22:13:41,115 workflow:INFO Building anatomical MRI QC workflow, datasets list: [u'sub-28853/anat/sub-28853_T1w.nii.gz']
2017-03-29 22:13:44,010 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-2~nd16.04+1 and AFNI_17.0.17 is available.
2017-03-29 22:13:46,638 interface:WARNING AFNI is outdated, detected version Debian-16.2.07~dfsg.1-2~nd16.04+1 and AFNI_17.0.17 is available.
2017-03-29 22:13:46,809 workflow:INFO Building fMRI QC workflow, datasets list: [u'sub-28853/func/sub-28853_task-rest_bold.nii.gz']
Traceback (most recent call last):
  File "/home/Thomas/miniconda2/bin/mriqc", line 11, in <module>
    load_entry_point('mriqc==99.99.99', 'console_scripts', 'mriqc')()
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/mriqc-99.99.99-py2.7.egg/mriqc/bin/mriqc_run.py", line 248, in main
    wf_list.append(build_workflow(dataset[mod], mod, settings=settings))
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/mriqc-99.99.99-py2.7.egg/mriqc/workflows/core.py", line 19, in build_workflow
    workflow = fmri_qc_workflow(dataset, settings=settings)
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/mriqc-99.99.99-py2.7.egg/mriqc/workflows/functional.py", line 104, in fmri_qc_workflow
    stop_idx=settings.get('stop_idx', None))
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/mriqc-99.99.99-py2.7.egg/mriqc/workflows/functional.py", line 532, in hmc_afni
    parameter_source="AFNI"),
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/nipype-0.13.0rc1-py2.7.egg/nipype/interfaces/base.py", line 776, in __init__
    self.inputs = self.input_spec(**inputs)
  File "/home/Thomas/miniconda2/lib/python2.7/site-packages/nipype-0.13.0rc1-py2.7.egg/nipype/interfaces/base.py", line 362, in __init__
    super(BaseTraitedSpec, self).__init__(**kwargs)
traits.trait_errors.TraitError: Cannot set the undefined 'parameter_source' attribute of a 'FramewiseDisplacementInputSpec' object.

Not sure what's causing that one. pip freeze output below:

pip freeze
cffi==1.9.1
click==6.7
conda==4.3.15
configparser==3.5.0
cryptography==1.7.1
cycler==0.10.0
decorator==4.0.11
dipy==0.11.0
enum34==1.1.6
funcsigs==1.0.2
functools32==3.2.3.post2
future==0.16.0
grabbit==0.0.5.1
h5py==2.6.0
html5lib==0.999999999
idna==2.2
ipaddress==1.0.18
isodate==0.5.4
Jinja2==2.9.5
keepalive==0.5
lxml==3.7.3
MarkupSafe==1.0
matplotlib==2.0.0
mock==2.0.0
mpmath==0.19
mriqc==99.99.99
networkx==1.11
nibabel==2.1.0
nilearn==0.2.6
nipy==0.4.1
nipype==0.13.0rc1
nitime==0.7
niworkflows==0.0.6.post3
nose==1.3.7
numpy==1.12.1
pandas==0.19.2
patsy==0.4.1
pbr==2.0.0
prov==1.5.0
psutil==5.2.1
py==1.4.33
pyasn1==0.1.9
pybids==0.1
pycosat==0.6.1
pycparser==2.17
pydicom==0.9.9
pydotplus==2.0.2
pyface==5.1.0
Pygments==2.2.0
pyOpenSSL==16.2.0
pyparsing==2.2.0
pytest==3.0.7
python-dateutil==2.6.0
pytz==2016.10
PyYAML==3.12
rdflib==4.2.2
requests==2.12.4
scikit-learn==0.18.1
scipy==0.19.0
seaborn==0.7.1
simplejson==3.10.0
six==1.10.0
sklearn==0.0
SPARQLWrapper==1.7.6
statsmodels==0.8.0
subprocess32==3.2.7
svgutils==0.2.0
sympy==1.0
tinycss==0.4
traits==4.6.0
traitsui==5.1.0
webencodings==0.5
xvfbwrapper==0.2.9
chrisgorgo commented 7 years ago

Have you tried running MRIQC via Docker or Singularity? You will avoid headaches with dependencies.

chrisgorgo commented 7 years ago

This looks like wrong nipype version. MRIQC depends on the not yet released version of nipype. You can install this and other missing dependencies from requirements.txt. I do however, recommend trying out Docker or Singularity. You will save time in the long run.

hermeckerogg commented 7 years ago

Couldn't install Docker on my setup for some reason involving the sudo add-apt-repository phase.

Have not tried it with singularity, will do so and close the issue if it works.

For the record however, I've tried to run mriqc with a fresh conda, minicoda, and just generic python 2.7.13 on the Windows Ubuntu 16.04 with both the pip installations and git cloned versions of mriqc (which correct me if I'm wrong, but from what you're saying should have the correct version of nipype) and the issues persists.

chrisgorgo commented 7 years ago

Docker does not work on Windows for Linux Subsystem. You should install it directly on Windows (see https://miykael.github.io/nipype_tutorial/notebooks/introduction_docker.html#Install-Docker).

hermeckerogg commented 7 years ago

I'll try that. Thank you.

oesteban commented 7 years ago

@hermeckerogg did you manage to run mriqc in docker?

I've been looking at your error above, and it seems to me that you are missing the bleeding edge version of nipype:

pip install git+https://github.com/nipy/nipype.git

I'll keep an eye on this if you have time to give it a try :)

Thanks!

hermeckerogg commented 7 years ago

Had some things come up so I haven't been able to try it on the (Windows) docker yet but its on my list between now and tomorrow.

Though I really would like to try this locally so I'll give the link provided git a shot after I try with the docker.

Thank you!

hermeckerogg commented 7 years ago

Sure its just a syntax error in how I have my files structured but I've been getting the following error on the Docker:

$ docker run -v /F/ABIDEII/ABIDEII-SDSU_1_BIDS:/data -v /F/ABIDEII/mriqcout:/scratch -w /scratch poldracklab/mriqc:latest /data /scratch/out participant --participant_label sub-28853 -w /scratch/work
time="2017-04-07T17:17:24-05:00" level=info msg="Unable to use system certificate pool: crypto/x509: system root pool is not available on Windows"
/usr/local/miniconda/lib/python3.6/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.
  "This module will be removed in 0.20.", DeprecationWarning)
2017-04-07 22:17:29,048 root:INFO Running MRIQC-0.9.1 (analysis_levels=[participant], participant_label=['sub-28853'])
        Settings={'bids_dir': '/data', 'write_graph': False, 'testing': False, 'hmc_afni': True, 'hmc_fsl': False, 'fft_spikes_detector': False, 'n_procs': 1, 'ants_nthreads': 6, 'output_dir': '/scratch/out', 'work_dir': '/scratch/work', 'verbose_reports': False, 'float32': False, 'deoblique': False, 'despike': False, 'correct_slice_timing': False, 'report_dir': '/scratch/out/reports'}
2017-04-07 22:17:29,057 root:WARNING No T1w scans were found in /data
2017-04-07 22:17:29,057 root:WARNING No bold scans were found in /data
2017-04-07 22:17:29,057 root:WARNING No T2w scans were found in /data
participant labels  ['^28853$']
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/mriqc", line 11, in <module>
    load_entry_point('mriqc', 'console_scripts', 'mriqc')()
  File "/opt/src/mriqc/mriqc/bin/mriqc_run.py", line 257, in main
    'BIDS-compliant.' % settings['bids_dir'])
RuntimeError: Error reading BIDS directory (/data), or the dataset is not BIDS-compliant.

I know the data is BIDS compliant, the validator confirmed it. ABIDEII-SDSU_1_BIDS_errors.txt

Any suggestions as to what I might be doing wrong?

oesteban commented 7 years ago

Can you post the output of tree /F/ABIDEII/ABIDEII-SDSU_1_BIDS ?

The command line looks good.

hermeckerogg commented 7 years ago

$ tree /F/ABIDEII/ABIDEII-SDSU_1_BIDS bash: tree: command not found

for some reason.

oesteban commented 7 years ago

and find /F/ABIDEII/ABIDEII-SDSU_1_BIDS ?

hermeckerogg commented 7 years ago 
$ find find /f/ABIDEII/ABIDEII-SDSU_1_BIDS
find: ‘find’: No such file or directory
/f/ABIDEII/ABIDEII-SDSU_1_BIDS
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/.bashrc
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/ABIDEII-SDSU_1_BIDS_errors.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/anat_qap.csv
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/dti_qap.csv
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/DWI_QA.sh
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/functional_qap.csv
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/mriqctest
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/mriqctest/derivatives
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/mriqctest/logs
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/mriqctest/reports
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/pathmatcher_report.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/SDSU_DTI_QA_Metrics.xlsx
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/SDSU_DWI_QCResults-IP_1_Data.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/SDSU_RestEPI_QA_Metrics.xlsx
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853/dwi/sub-28853_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853/dwi/sub-28853_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853/dwi/sub-28853_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28853/dwi/sub-28853_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854/dwi/sub-28854_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854/dwi/sub-28854_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854/dwi/sub-28854_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28854/dwi/sub-28854_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855/dwi/sub-28855_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855/dwi/sub-28855_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855/dwi/sub-28855_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28855/dwi/sub-28855_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857/dwi/sub-28857_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857/dwi/sub-28857_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857/dwi/sub-28857_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28857/dwi/sub-28857_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860/dwi/sub-28860_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860/dwi/sub-28860_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860/dwi/sub-28860_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28860/dwi/sub-28860_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861/dwi/sub-28861_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861/dwi/sub-28861_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861/dwi/sub-28861_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28861/dwi/sub-28861_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862/dwi/sub-28862_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862/dwi/sub-28862_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862/dwi/sub-28862_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28862/dwi/sub-28862_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863/dwi/sub-28863_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863/dwi/sub-28863_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863/dwi/sub-28863_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28863/dwi/sub-28863_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864/dwi/sub-28864_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864/dwi/sub-28864_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864/dwi/sub-28864_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28864/dwi/sub-28864_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865/dwi/sub-28865_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865/dwi/sub-28865_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865/dwi/sub-28865_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28865/dwi/sub-28865_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866/dwi/sub-28866_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866/dwi/sub-28866_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866/dwi/sub-28866_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28866/dwi/sub-28866_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867/dwi/sub-28867_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867/dwi/sub-28867_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867/dwi/sub-28867_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28867/dwi/sub-28867_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868/dwi/sub-28868_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868/dwi/sub-28868_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868/dwi/sub-28868_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28868/dwi/sub-28868_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869/dwi/sub-28869_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869/dwi/sub-28869_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869/dwi/sub-28869_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28869/dwi/sub-28869_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870/dwi/sub-28870_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870/dwi/sub-28870_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870/dwi/sub-28870_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28870/dwi/sub-28870_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872/dwi/sub-28872_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872/dwi/sub-28872_dwi_qamask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872/dwi/sub-28872_dwi_tsnrmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28872/dwi/sub-28872_SDSU_QAresults.txt
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28873
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28873/dwi
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28873/dwi/sub-28873_dwi_clipmask.nii
/f/ABIDEII/ABIDEII-SDSU_1_BIDS/derivatives/sub-28873/dwi/sub-28873_dwi_qamask.nii
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oesteban commented 7 years ago

Thanks, looks ok indeed. Let's see what mriqc is seeing from within the container:

docker run -v /F/ABIDEII/ABIDEII-SDSU_1_BIDS:/data --entrypoint=/bin/bash poldracklab/mriqc:latest find /data
hermeckerogg commented 7 years ago

This is what that command returns:

$ docker run -v /f/ABIDEII/ABIDEII-SDSU_1_BIDS:/data --entrypoint=/bin/bash poldracklab/mriqc:latest find /data time="2017-04-08T19:53:08-05:00" level=info msg="Unable to use system certificate pool: crypto/x509: system root pool is not available on Windows" /usr/bin/find: /usr/bin/find: cannot execute binary file

hermeckerogg commented 7 years ago

I get a similar error with the docker now actually. Which is strange because the package seemed to have install just fine first time I ran it.

docker run -it poldracklab/mriqc:latest -v time="2017-04-10T13:59:17-05:00" level=info msg="Unable to use system certificate pool: crypto/x509: system root pool is not available on Windows" /usr/local/miniconda/lib/python3.6/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20.

chrisgorgo commented 7 years ago

This DeprecationWarning is normal and can be ignored.

hermeckerogg commented 7 years ago

And the following error from @oesteban 's suggestion?

level=info msg="Unable to use system certificate pool: crypto/x509: system root pool is not available on Windows" /usr/bin/find: /usr/bin/find: cannot execute binary file

chrisgorgo commented 7 years ago

I'm not sure why this is happening, but this should work:

$ docker run -v /f/ABIDEII/ABIDEII-SDSU_1_BIDS:/data --entrypoint=find poldracklab/mriqc:0.9.1 /data

oesteban commented 7 years ago

@hermeckerogg that "Unable to use system certificate pool: crypto/x509: system root pool is not available on Windows" may indicate that you can't access / in you docker container. But I have no idea of docker on Windows. -- let's see if @chrisfilo's suggestion makes the trick.

chrisgorgo commented 7 years ago

I doubt it: https://github.com/docker/docker/issues/30450

hermeckerogg commented 7 years ago

So played around with a few things.

I had Docker 17.03 installed so I upgraded to v17.04.0-ce and tweeked the settings for the Vbox "default" that seems to have fixed the Windows system root pool error.

The command @chrisfilo suggested now returns the following: $ docker run -v /f/ABIDEII/ABIDEII-SDSU_1_BIDS:/data --entrypoint=find poldracklab/mriqc:0.9.1 /data /data

So it looks like its reading from where its supposed to be at least.

However, the command still throws that same non-BIDS error:

$ docker run -v /f/ABIDEII/ABIDEII-SDSU_1_BIDS:/data -v /F/ABIDEII/mriqcout:/scratch -w /scratch poldracklab/mriqc:late st /data /scratch/out participant --participant_label sub-28853 -w /scratch/work /usr/local/miniconda/lib/python3.6/site-packages/sklearn/cross_validation.py:44: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20. "This module will be removed in 0.20.", DeprecationWarning) 2017-04-11 18:47:35,591 root:INFO Running MRIQC-0.9.1 (analysis_levels=[participant], participant_label=['sub-28853']) Settings={'bids_dir': '/data', 'write_graph': False, 'testing': False, 'hmc_afni': True, 'hmc_fsl': False, 'fft_spikes_detector': False, 'n_procs': 1, 'ants_nthreads': 6, 'output_dir': '/scratch/out', 'work_dir': '/scratch/work', 'verbose_reports': False, 'float32': False, 'deoblique': False, 'despike': False, 'correct_slice_timing': False, 'report_dir': '/scratch/out/reports'} 2017-04-11 18:47:35,600 root:WARNING No T1w scans were found in /data 2017-04-11 18:47:35,600 root:WARNING No bold scans were found in /data 2017-04-11 18:47:35,600 root:WARNING No T2w scans were found in /data participant labels ['^28853$'] Traceback (most recent call last): File "/usr/local/miniconda/bin/mriqc", line 11, in load_entry_point('mriqc', 'console_scripts', 'mriqc')() File "/opt/src/mriqc/mriqc/bin/mriqc_run.py", line 257, in main 'BIDS-compliant.' % settings['bids_dir']) RuntimeError: Error reading BIDS directory (/data), or the dataset is not BIDS-compliant.

Maybe its not actually passing the files to the data folder?

chrisgorgo commented 7 years ago

$ docker run -v /f/ABIDEII/ABIDEII-SDSU_1_BIDS:/data --entrypoint=find poldracklab/mriqc:0.9.1 /data /data

So it looks like its reading from where its supposed to be at least.

Nope. It's just showing an empty folder. This command should list all the files in your dataset.

Did you enable sharing of disk "F" in docker settings?

hermeckerogg commented 7 years ago

Also in response to @oesteban 's post earlier about using the latest Nipype on the local install.

Did that, same error still occurs. This is even after checking the requirments.txt for both mriqc and nipype and all of them seem to be satisfied.

Now I'm wondering if it its the way the workflow is trying to input the data or if its an issue with ANTs.

crashfiles.zip

hermeckerogg commented 7 years ago

Didn't think of that.

Let me move it locally for ease of use at the moment and see if it can read it and if can then I'll set up sharing on F.

hermeckerogg commented 7 years ago

So good news:

Moved it locally (and in the process discovered a syntax error in the command I was running).

Took a minute to run locally but it worked!

Happy to consider the issue closed.

While I'm on on the subject though, is there a recommended way to call the output of pip freeze and the environment variables of the container? I'm entertaining the idea of making a virtual env on our cluster for this.

hermeckerogg commented 7 years ago

**Ran locally using the Docker.

chrisgorgo commented 7 years ago

I'm glad it worked!

We recommend using Singularity on clusters (more details http://bids-apps.neuroimaging.io/tutorial/)

hermeckerogg commented 7 years ago

Thank you!