[MINC-users] MINC tools for diffusion weighted images

[Andrew Janke]

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.

>  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!

>  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).

>  5. export the DWI (and DTI) volume to other well-known formats (nifti
>     or NRRD mostly) for further processing.

No idea on that one.

> 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.

> 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.


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