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bids-apps / example

This an example app that can serve as a template.

Home Page:https://doi.org/10.1371/journal.pcbi.1005209

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example produces no sensible output

yarikoptic opened this issue · comments

commented

There was a concern about bids-apps and git-annex'es symlinks. I have tried to run the BIDS-app/example on two sample datasets (ds000001 and 5 from openneuro) to arrive to the same results regardless of the files being symlinks or not. Since ds005 was originally "demonstrated" in README.md here is full protocol for its run:

smaug:/mnt/datasets/datalad/tmp
$> datalad install -g -s ///openneuro/ds000005      
[INFO   ] Cloning http://datasets.datalad.org/openneuro/ds000005 [1 other candidates] into '/mnt/datasets/datalad/tmp/ds000005' 
[INFO   ] access to dataset sibling "s3-PRIVATE" not auto-enabled, enable with:                                                                                                                                         
| 		datalad siblings -d "/mnt/datasets/datalad/tmp/ds000005" enable -s s3-PRIVATE 
install(ok): /mnt/datasets/datalad/tmp/ds000005 (dataset)
action summary:                                                                                                                                                                                                         
  get (ok: 81)                                                                                                                                                                                                          
  install (ok: 1)                                                                                                                                                                                                       
datalad install -g -s ///openneuro/ds000005  85.82s user 22.10s system 365% cpu 29.496 

$> docker run -i --rm -v $PWD/ds000005:/bids_dataset:ro -v $PWD/:/outputs bids/example /bids_dataset /outputs group        
	1: This file is not part of the BIDS specification, make sure it isn't included in the dataset by accident. Data derivatives (processed data) should be placed in /derivatives folder. (code: 1 - NOT_INCLUDED)
		/.datalad/.gitattributes
			Evidence: .gitattributes
		/.datalad/config
			Evidence: config
		/.gitattributes
			Evidence: .gitattributes

	2: You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)
		/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
		/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
		/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
		/sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz
		/sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz
		/sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz
		/sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz
		/sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz
		/sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz
		/sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz
		... and 38 more files having this issue (Use --verbose to see them all).

        Summary:                 Available Tasks:          Available Modalities: 
        498 Files, 3.54GB        mixed-gambles task        T1w                   
        16 - Subjects                                      inplaneT2             
        1 - Session                                        bold                  


/run.py:86: RuntimeWarning: Mean of empty slice.
  fp.write("Average brain size is %g voxels"%numpy.array(brain_sizes).mean())
/usr/local/lib/python3.4/dist-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)

$> cat avg_brain_size.txt 
Average brain size is nan voxels%

so would be nice to have example to provide sensible measure in the output