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Filling up README and provided a copy of Singularity
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yarikoptic committed Feb 5, 2018
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MIT License

Copyright (c) 2018 Center for Reproducible Neuroimaging Computation
Copyright (c) 2016-2018 Center for Reproducible Neuroimaging Computation

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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# reproin
A setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners
# ReproIn

This project is a part of the suite. Its goal is to provide a
turnkey flexible setup for automatic generation of shareable,
version-controlled BIDS datasets from MR scanners. To not reinvent the wheel,
all actual software development is largely done through contribution to
existing software projects:

- [HeuDiConv]( -
a flexible DICOM converter for organizing brain imaging data into structured
directory layouts.
ReproIn [heuristic] was developed and now is shipped within HeuDiConv,
so it could be used independently of the ReproIn setup on any HeuDiConv
installation (specify `-f reproin` to heudiconv call).
- [DataLad](
a modular version control platform and distribution for both code and
data. DataLad support was contributed to HeuDiConv, and could be
enabled by adding `--datalad` option to the `heudiconv` call.

The recommended invocation for the heudiconv is

$ heudiconv -c dcm2niix -f reproin --bids --datalad -o OUTPUT --files INPUT
to convert all found in `INPUT` DICOMs and place then within the
hierarchy of DataLad datasets rooted at `OUTPUT`.

## Specification

The header of the [heuristic] file describes details of the
specification on how to organize and name study sequences at MR console.

## Sample converted datasets

You could find sample datasets with original DICOMs

- [///dbic/QA]( is a publicly
available DataLad dataset with historical data on QA scans from DBIC.
You could use DICOM tarballs under `sourcedata/` for your sample
TODO: add information from which date it is with scout DICOMs having
session identifier
- [///dicoms/dartmouth-phantoms](
provides a collection of datasets acquired at [DBIC] to establish
ReproIn specification. Some earlier accessions might not be following
the specification.
provides a basic example of multi-subject and multi-session acquisition.

## Containers

This repository provides a [Singularity](./Singualarity) environment
definition file used to generate a complete environment needed to run
a conversion

## TODOs/WiP

- [ ] adding pre-configured DICOM received for fully turnkey deployments
- [ ] [heudiconv-monitor] to fully automate conversion of the incoming
- [ ] [BIDS dataset manipulation helper](

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# Copyright (c) 2015-2016, Gregory M. Kurtzer. All rights reserved.
# Changes for NeuroDebian/ReproIn setup are Copyright (c) 2017-2018 Yaroslav Halchenko.
# The purpose of the environment is to provide a complete suite for running
# heudiconv on the INBOX server to provide conversion into BIDS layout.
# ATM it does not ship heudiconv itself which would be accessed directly
# from the main drive for now.
# "Singularity" Copyright (c) 2016, The Regents of the University of California,
# through Lawrence Berkeley National Laboratory (subject to receipt of any
# required approvals from the U.S. Dept. of Energy). All rights reserved.

# Notes:
# - Due to
# bootstrapping leads to non-usable/non-removable-without-reboot
# image due to some rogue run away processes.
# This line could help to kill them but should be used with caution
# since could kill other unrelated processes
# grep -l loop /proc/*/mountinfo | sed -e 's,/proc/\(.*\)/.*,\1,g' | while read pid; do sudo kill $pid; done
# Changes/version
# 0.0.20180205
# - Rebuilt to update dcm2niix etc
# - Boosted bids-validator version to 0.25.6
# 0.0.20170928
# - require current bids validator 0.23.2, but in general regenerate to update datalad and dcm2niix
# - install dcmtk for dcmdump

BootStrap: debootstrap
#OSVersion: stable
# needs nipype 0.12.1 but that one didn't build for stable since needs python-prov...
# so trying stretch
OSVersion: stretch

# so if image is executed we just enter the environment
echo "Welcome to the ReproIn (AKA formerly DBIC-BIDS) environment"

echo "Configuring the environment"
apt-get update
apt-get -y install eatmydata
eatmydata apt-get -y install vim wget strace time ncdu gnupg curl procps
wget -q -O/tmp/nd-configurerepo
bash /tmp/nd-configurerepo
chmod a+r -R /etc/apt
eatmydata apt-get -y install git-annex-standalone datalad python-nipype virtualenv dcm2niix python-dcmstack python-configparser python-funcsigs python-pytest dcmtk

# for bids-validator
# not present in stretch, see
# eatmydata apt-get install -y npm
curl -sL | bash - && \
eatmydata apt-get install -y nodejs
npm install -g bids-validator@0.25.6
chmod a+rX -R /usr/lib/node_modules/

chmod a+rX -R /etc/apt/sources.list.d
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
apt-get clean

# and wipe out apt lists since not to be used RW for further tuning
# find /var/lib/apt/lists/ -type f -delete
# /usr/bin/find /var/lib/apt/lists/ -type f -name \*Packages\* -o -name \*Contents\*
# complicates later interrogation - thus disabled

# Create some bind mount directories present on rolando
mkdir -p /afs /inbox
chmod a+rX /afs /inbox

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