= SPM DTI toolbox =

This is a toolbox for playing with DTI data, including data import and export in DICOM, SPM and FSL format, creating mask images, and diagnosing slice artfacts, such as the DtiSpikingArtefact. It automates many of the preprocessing steps in [CbuImaging:DiffusionFdtNotes]

== In use ==

First, get a version of the code - for now use the development versions - as below.

Then, to convert some DICOM FSL data to FSL format, try this:

{{{
dt_dicom_to_fsl
}}}

You should find, after following a few prompts, that you have, in your
selected output directory, two new directories:

 * spm_dti (containing the DICOM-NIFTI converted SPM files and diffusion directions)
 * fdt (containing data ready for input into the FSL fdt tool)

Let me know of any problems, it's in early testing.

== To install a development code copy on your system ==

You will need subversion, and three repositories, like this:

{{{
cd my_directory
svn co http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti
svn co http://imaging.mrc-cbu.cam.ac.uk/svn/utilities/devel utilities
# And for testing
svn co http://imaging.mrc-cbu.cam.ac.uk/svn/testing/devel testing
}}}

Put all three of cbudti, utilities and (optionally) testing on your matlab path
 
== Subversion repository ==

At: http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel

For example, to get a copy of the current state of the development code:

`svn export http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti`

(this results in a new `cbudti` directory containing the code.  To use it, put it on your matlab path (`addpath /your/directory/cbudti`).

To check out a versioned copy for editing or reviewing changes:

`svn co http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti`

Then (if you have permission) edit some file.

Then:

`svn commit -m 'A comment'`

And:

`cd cbudti; svn update`

to get the latest repository data into your working copy in the `cbudti` subdirectory.

MatthewBrett