[Mrtrix-discussion] nii conversion and general questions

[Donald Tournier]

Hi Kerstin,

Glad to hear the new release will be useful. In answer to your questions:

> 1) I noticed that the transformation in the header file when converting from
> *.nii is not identity any more (as is used to be when converting from
> ANALYZE). I assume I can therefore not use the bvecs I use for FSL-analysis?
> Would I get the gradient scheme directly from DICOM then? On the other hand,
> if I would use mrconvert to convert from *.mih to *.nii, could I then use
> the *.mih gradient scheme for FSL-analysis? Or do I need 2 sets of bvecs,
> one for mrtrix, one for FSL?

This is actually the main reason to implement NIfTI support: the
Analyse header has no way of storing the transformation. What you see
in that field when reading an Analyse image (or any image derived from
one) using MRtrix (or FSL) is a default transform (the identity)
assigned by the software rather than read from the headers. Any image
derived or converted from an Analyse image will be assigned this
default header. I would recommend avoiding the Analyse format for that
reason.

Whether you can use the same bvecs is a slightly trickier question to
answer. As far as I know, the bvecs I get from the DICOM headers are
specified relative to real space, and this is what MRtrix also
assumes. I'm not sure how FSL works from that point of view. If your
DW images are all acquired as straight axials, then there should be no
problem using the same bvecs for both (since there is no rotation
between the Analyse & NIfTI images, just translation). On the other
hand, if they are tilted, then I'm guessing that you should NOT be
using the bvecs obtained from MRtrix to process Analyse images with
FSL (or MRtrix for that matter). I have no idea how FSL deals with
NIfTI images if there is any rotations in the transform.

In short, I'm not sure what bvecs you should use with FSL. On the
other hand, you should definitely use the DICOM bvecs for MRtrix
processing, if they are available. Remember that if you intend to
coregister your data, you should leave the DWI and related images
(i.e. FA, CSD, etc) unmodified - you should register other images to
them, rather than the other way around. There's some discussion about
that in the Frequently Asked Questions in the new docs.



> 2) During CSD computation, I sometimes get a message "csdeconv: failed to
> converge". Should I be worried about that and reduce lmax? The computation
> continues after this message, and the results look reasonable to me. My
> dataset is 65 directions, b3000, 2 averages, lmax 8. This is the command I
> ran:
>
> $ csdeconv ../data/data.mih -grad ../data/encoding.b -lmax 8 response.txt
> -mask ../data/nodif_brain_mask.mih CSD8.mih
>
> csdeconv: performing constrained spherical deconvolution...  63%csdeconv:
> failed to converge
> csdeconv: performing constrained spherical deconvolution... 100%

This is also now discussed in the Frequently Asked Questions. If you
only get one message, this means only one voxel is affected, and is
unlikely to be in white matter anyway. I wouldn't worry too much about
that unless you get dozens of these messages per data set.

There are actually two different reasons why csdeconv might fail to
converge. One is that it has gone over the maximum number of
iterations (default is 50). This usually happens because it is
oscillating between two equally suitable solutions. In this case, you
end up with whichever solution was last computed. The other reason is
that it failed to identify enough negative directions to make the
problem tractable. This can only happens when performing a
super-resolved reconstruction (in your case, lmax >= 10). In this
case, that voxel is left blank - you end up with a hole in the data.
Thankfully, these problems tend to happen in non-brain or grey matter
voxels, so are not usually a problem for tractography. However, if you
find you get lots of these messages, there may be something going on
that needs to be investigated further.



> 3) Is it possible to extract the fibre orientation and fraction information
> from the CSD-file?

The command 'find_SH_peaks' is what you're looking for.

Hope that helps.
Cheers,

Donald.


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078