[MINC-users] MINC tools for diffusion weighted images

[Ilana Leppert]

Hi,
The toolkit you mention (mincdiffusion, developed by Jennifer Campbell), is
in the process of being packaged and with Vlad's help, we plan to include
it in the standard minc distribution.


On Fri, Sep 27, 2013 at 2:16 AM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Jon,
>
> > What sorts of tools are there for working with diffusion weighted images
> > in MINC?
> >
> > Specifically, my wish list includes tools enabling me to:
> >  1. convert the DWI from our raw dicoms to minc format preserving
> >     diffusion parameters
>
> dcm2mnc should preserve this for you. Take a look at the GIT history
> of dcm2mnc and you will see a lot of commits around this from Bruce
> Pikes group.
>
> >  2. merge multiple DWI acquisitions for single subject
>
> Depends on what level. But no pre-canned methods in MINC that I know
> of for public download.
>

We do a linear registration between runs and concatenate the volumes and
diffusion header information.


> >  3. perform registration of the DWI image to a structural scan (updating
> >     directions)
>
> Not that I know of. But again, this depends on the method, are you
> correcting the raw data or the first order tensor approximation? if
> the raw data, I can't imagine this being too hard to do with a few
> judicious calls to minccalc, when doing this are you also planning on
> doing some form of mass preservation for nonlinear deformations? If so
> this can be achieved by using mincblob -determinant on the resulting
> field and multiplying the result with the resampled volume. But again,
> no pre-canned tool but something that could be simply scripted using
> python/perl. Jason will no doubt point you to pyminc!
>


This is part of the pre-processing, but only linear registrations are
implemented. A program called 'transform_diff_dirs' takes care of updating
the directions.


> >  4. estimate a diffusion tensor
>
> The code I released for this many years ago when first order tensor
> approximations were all the rage (mincdti) is still there and works.
> Others have matlab toolboxes and other things around this, I don't
> know of a public release of these though. Perhaps they can chime in
> here. (Illana and Jennifer come to mind).
>

Yes, we have 'minctensor.pl', which uses matlab, which outputs the tensor,
FA, MD and a color-coded by direction RGB.

>
> >  5. export the DWI (and DTI) volume to other well-known formats (nifti
> >     or NRRD mostly) for further processing.
>
> No idea on that one.
>

I have found mnc2nii to work well, even for diffusion (you'll have to grab
the diffusion information from the header). Vlad worked on some code using
ITK, which can convert back and forth from NRRD. Some DTI volumes
(eigenvectors, eigenvalues) might require some extra manipulation because
different software expect different formats.

>
> > From my searching so far it looks like there is a toolkit[1] for MINC
> > that should do most of the above, but I'm not sure if it is a) still
> > maintained, or b) available to the public (seems one must have a BIC
> > username to check out the source?).  There is also the mincdti
> > program[2] but I believe that only estimates a tensor.
>
> Correct, only a first order tensor, and then FA, ISO, etc from that.
>

We have some tools for estimating multiple fiber populations per voxel
(Spherical Deconvolution) as well as tracking using FACT or the maxima from
of the fiber ODF resulting from the deconvolution. There are also some nice
3D visualization tools.

>
> > What are my other options? With the minc integration into ITK are there
> > perhaps ITK-based toolkits you could recommend?
>
> ITK is probably a good vector.
>
>
> a
>

I hope that helps, maybe Jen would like to add some more info...
Ilana

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