#ReadMe for DTI QA 

AFNI and FSL must be installed and in your PATH environment
 
To execute the quality assurance scripts, you will need download the scripts and extract all scripts to the same directory. In addition, you will need the full paths to:
 
a) the raw DTI nifti image you wish to analyze (nifti)
b) corresponding bval file (bval)
c) corresponding bvec file (bvec)
d) output path and output file name
 
The quality assurance script is then called utilizing the above variables in the following command (all necessary subscripts should run as long as they are in the script folder and neuroimaging tools are in your PATH enviornment):

/path/to/your/scripts/folder/qa_dti_v1.sh [nifti] [bval] [bvec] [outfile]

 For   example: 
 
/my/scripts/folder/qa_dti_v1.sh /my/data/folder/subjects/AAAA/DTI/nifti/rawDTI64.nii.gz /my/data/folder/subjects/AAAA/DTI/nifti/bvalfile.bval /my/data/folder/subjects/AAAA/DTI/nifti/bvecfile.bvec /my/output/data/folder/suject/DTI/qa/AAAA_dti.qa