https://github.com/repronim/simple-qa
Simple QA
https://github.com/repronim/simple-qa
Last synced: about 1 year ago
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Simple QA
- Host: GitHub
- URL: https://github.com/repronim/simple-qa
- Owner: ReproNim
- Created: 2016-11-11T17:47:20.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-12-08T19:14:29.000Z (over 9 years ago)
- Last Synced: 2025-04-09T21:48:54.183Z (about 1 year ago)
- Language: Shell
- Size: 7.81 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
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README
ReproNim Simple QA
==================
This is a sample end-user script for testing ReproNim. It is in fact
fairly not-simple in that a complete run requires:
- AFNI (https://afni.nimh.nih.gov/, NeuroDebian)
- BXH/XCEDE Tools (https://www.nitrc.org/projects/bxh_xcede_tools)
- FreeSurfer (http://surfer.nmr.mgh.harvard.edu/)
- fsutils (https://github.com/chaselgrove/fsutils, PyPi)
- ImageMagick (http://www.imagemagick.org/script/index.php, MacPorts,
Debian)
- Jinja2 (Debian, PyPi)
- nibabel (NeuroDebian, PyPi)
- R (https://www.r-project.org/, Debian)
Install the script by putting the contents of this repository in a
directory and setting RN_QA_DIR to this directory.
Run the script with a structural volume, a time-series volume, and an
output directory that doesn't exist yet:
::
$RN_QA_DIR/rn_qa anat.nii.gz time_series.nii.gz /path/to/output/directory
The results and intermediate data from the analysis are placed in the
output directory. The ostensible final result is in ``html/index.html``.
The actual purpose of this analysis is as a test of ReproNim
and being able to reproduce an analysis with several component parts,
so the real output of interest is the file ``meta`` in the output
directory, which tells which software (including versions) was available
to be used in the analysis.