rwblair

The current version of docker in tha Amazon Linux repositiories is 1.7.1. This version has a limit of 10gb for images unless dm.basesize
is configured on docker startup. In the interest of getting the site back online as quick as possible a number of workarounds of this
limit can be seen in docker-compose.yml and fs_docker/Dockerfile.

The wget and untar in fs_docker/Dockerfile would cause the image to run out of space on being built. To remedy this I pre downloaded the
freesurfer code and had it added to the image directly. To further reduce the space impact of the freesurfer install the following
directories were removed from freesurfer/subjects:
bert  cvs_avg35  cvs_avg35_inMNI152  lh.EC_average  rh.EC_average  V1_average

There was an issue with transformations in pycortex taking up large amounts of space. A copy of the pycortex directory was made and moved

rwblair

	1: Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme. (code: 38)
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme.
			Evidence: Subject: sub-13; Missing file: /ses-1/fmap/sub-13_ses-1_run-1_magnitude2.nii.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme.
			Evidence: Subject: sub-19; Missing file: /ses-1/func/sub-19_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme.
			Evidence: Subject: sub-1

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	1: Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme. (code: 38)
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-13; Missing file: /ses-1/fmap/sub-13_ses-1_run-1_magnitude2.nii.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-19; Missing file: /ses-1/func/sub-19_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-19; Missing file: /ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz

	2: Some nifti files have non-normative header field values. (code: 39)
		/sub-11/ses-1/func/sub-11_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz

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~/projects/bids-validator $ bin/bids-validator ~/Downloads/7t_trt
	1: Not all sessions contain the same corresponding files. Each session should contain the same number of files with the same naming scheme. (code: 38)
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-13; Missing file: /ses-1/fmap/sub-13_ses-1_run-1_magnitude2.nii.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-19; Missing file: /ses-1/func/sub-19_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz
		/sub-19/ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz
			Evidence: Subject: sub-19; Missing file: /ses-1/func/sub-19_ses-1_task-rest_acq-prefrontal_physio.tsv.gz

	2: Some nifti files have non-normative header field values. (code: 39)

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~/projects/nipype/nipype/interfaces/ants $ pip freeze
click==6.6
configparser==3.5.0
cycler==0.10.0
decorator==4.0.10
doctest-ignore-unicode==0.1.2
funcsigs==1.0.2
future==0.15.2
isodate==0.5.4
lxml==3.6.4

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~/projects/nipype $ make check-before-commit 
Checking specs and autogenerating spec tests
python tools/checkspecs.py
161209-14:23:38,529 interface WARNING:
         VTK was not found
161209-14:23:38,529 interface WARNING:
         tvtk wasn't found
FILMGLS has nonautotest
nipype.interfaces.ants.utils:CreateJacobianDeterminantImage:Inputs:doLogJacobian:mandatory=False
nipype.interfaces.ants.utils:CreateJacobianDeterminantImage:Inputs:useGeometric:mandatory=False

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# Sphinx version: 1.4.6
# Python version: 3.5.2 (CPython)
# Docutils version: 0.12 release
# Jinja2 version: 2.8
# Last messages:

# Loaded extensions:
Traceback (most recent call last):
  File "/home/rwblair/.anaconda3/lib/python3.5/site-packages/Sphinx-1.4.6-py3.5.egg/sphinx/cmdline.py", line 243, in main
    opts.warningiserror, opts.tags, opts.verbosity, opts.jobs)

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~/projects/nipype $ python
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import future
>>> future.__version__
'0.15.2'

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from py2neo import Graph, Node, Relationship

graph = Graph("http://192.168.99.100:7474/db/data/")

# list all concepts
def list_concepts():
    concepts = graph.cypher.execute("MATCH (c:concept) RETURN c")
    return concepts

concepts = list_concepts()

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= The Cognitive Atlas
:neo4j-version: 2.0.0
:author: Poldracklab
:twitter: @vsoch
:tags: cognitive:concepts:psychology:neuroscience

'''

View task: adaptive n-back task