= BDP Add-ons =
This page lists some utility functions which could be useful for data processing with [[http://brainsuite.org/processing/diffusion/|BrainSuite Diffusion Pipeline (BDP)]]. BDP is a part of BrainSuite and is geared towards analysis with diffusion MRI data. Most of the utilities listed here are developed using MATLAB R2012a and can be used inside MATLAB, unless otherwise mentioned. 

 * Merge multiple set of diffusion datasets
 * [[#eig2nifti|Eigen file (.eig) to NIfTI converter]]

<<Anchor(eig2nifti)>><<BR>><<BR>>
==  Eigen file (.eig) to NIfTI converter ==

{{{eig2nifti}}} converts {{{.eig.nii.gz}}} files saved by [[BrainSuite|BrainSuite Diffusion Pipeline (BDP)]] to standard NIfTI-1 format. It takes {{{.eig.nii.gz}}} file as input and writes out corresponding eigenvector and eigenvalue files in standard NIfTI-1 format.

'''Syntax'''
{{{
eig2nifti(input_eig_file, output_base)
}}}
where, {{{input_eig_file}}} is a character array of input filename ({{{.eig.nii.gz}}}) and {{{output_base}}} is character array of file-prefix for output filenames. Following example shows {{{eig2nifti}}} in action and explains the output files:  
{{{
>> eig2nifti('2467264c.dwi.RAS.correct.eig.nii.gz', '2467264c.tensor')
Reading eig file...Done
Saving files...
Saved V1 file: 2467264c.tensor.V1.nii.gz
Saved V2 file: 2467264c.tensor.V2.nii.gz
Saved V3 file: 2467264c.tensor.V3.nii.gz
Saved L1 file: 2467264c.tensor.L1.nii.gz
Saved L2 file: 2467264c.tensor.L2.nii.gz
Saved L3 file: 2467264c.tensor.L3.nii.gz
}}}
where {{{L1 file}}} contains the largest eigenvalues with corresponding eigenvector saved in {{{V1 file}}}. Similarly, {{{L2 file}}} contains the second largest eigenvalues with corresponding eigenvector saved in {{{V2 file}}} followed by {{{L3 file}}} and {{{V3 file}}}. All eigenvalue files ({{{L1,L2,L3}}}) are 3D volume while eigenvector files ({{{V1,V2,V3}}}) are 4D volume with last dimension containing the eigenvectors.

{{{eig2nifti}}} depends on several other functions which are included along with the download zip. All files should be added to the MATLAB path. See included {{{sample_eig2nifti.m}}} for another example of running {{{eig2nifti}}}.

=== Download Links ===

 * [[http://neuroimage.usc.edu/resources/eig2nifti.zip|eig2nifti.zip]]
Last Modified: Oct 9, 2013

'''Authors:''' [[Members|Chitresh Bhushan]] 

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