help.txt

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% Read a JSON object, a JSON file, or a directory containing a json file
% and run dtiInit inside of a docker container (scitran/dtiinit).
%
%
% INPUTS:
%       json - a JSON string, a JSON file, or a directory containing a json
%              file, in the following format (Note that 'input_dir' and
%              'output_dir' are the only REQUIRED inputs)
%
% OUTPUTS:
%       A docker run produces a zip file containing all of the outputs
%       from the algorithm. The name of the output zip file is:
%           'dtiInit[date-time].zip'
%
%
% JSON SCHEMA:
%       Below is an example JSON file with the defaults show for 'params'.
%       See dtiInitParams.m for more info regarding params. Note that
%       "input_dir" and "output_dir" are required and must be in the
%       context of the container.
%
%             {
%                 "input_dir": "/input",
%                 "output_dir": "/output",
%                 "dwi_file": "",
%                 "bvec_file": "",
%                 "bval_file": "",
%                 "t1_file": "",
%                 "params":
%                     {
%                         "bvalue": "",
%                         "gradDirsCode": "",
%                         "clobber": 0,
%                         "dt6BaseName": "",
%                         "flipLrApFlag": 0,
%                         "numBootStrapSamples": 500,
%                         "fitMethod": "ls",
%                         "nStep": 50,
%                         "eddyCorrect": 1,
%                         "excludeVols": "",
%                         "bsplineInterpFlag": 0,
%                         "phaseEncodeDir": "",
%                         "dwOutMm": [2, 2, 2],
%                         "rotateBvecsWithRx": 0,
%                         "rotateBvecsWithCanXform": 0,
%                         "bvecsFile": "",
%                         "bvalsFile": "",
%                         "noiseCalcMethod": "b0",
%                         "outDir": "/output/"
%                     }
%             }
%
%
% REQUIRED INPUTS:
%       'input_dir' and 'output_dir' are the only required inputs.
%
%
% HELP:
%       If 'help', '-h', '--help', or nothing (nargin==0), is passed in
%       this help will be displayed.
%
%
% USAGE:
%       Pass in a JSON file, a JSON text string, or a path to a directory
%       containing a JSON file to the docker container to initiate a
%       dtiInit processing run (see INPUT section for JSON schema):
%
%       % Using a JSON file
%        docker run --rm -ti -v `pwd`/input:/input -v `pwd`/output:/output scitran/dtiinit /input/<JSON_filename>.json
%
%       % Using a JSON string
%        docker run --rm -ti -v `pwd`/input:/input -v `pwd`/output:/output scitran/dtiinit '{"input_dir":"/input", "output_dir": "/output"}'
%
%       % Using a directory (in the container), containing a JSON (.json)
%        docker run --rm -ti -v `pwd`/input:/input -v `pwd`/output:/output scitran/dtiinit /input/
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%
%