[Mrtrix-discussion] nii conversion and general questions

[Donald Tournier]

Hi Vinod,

I completely agree, a 3D viewer would be great, and it is definitely
on the wishlist. Unfortunately, I'm far too busy at the moment to work
on that. Maybe in a few months' time...

In the meantime, you can get a kind of '3D feel' for your tracks this way:

1. load an image
2. adjust the contrast/brightness until the image is completely black
3. load your tracks using the tractography sidebar
4. untick the 'crop to slab' option in the tractography sidebar
5. untick the 'lock to image axes' option in the View menu
6. rotate your tracks around by holding down the Ctrl key while
dragging the mouse with the left or middle button down (left button:
rotate within plane, middle button: rotate out of plane).

It takes a little getting used to, but the tracks look good
(especially with the 'depth blend' option and the opacity lowered a
touch).

Let me know if that helps.
Cheers,

Donald.


On Mon, Sep 8, 2008 at 6:12 AM, vinod kumar <mail.vinod at yahoo.com> wrote:
> Hi Donald,
>
> how are you. I hope you had nice weekend.
>
> Thanx for new version with NIFTI support.  New docs have good FAQ section. I
> read all today. At the moment I am in the way to improve bit more SNR, need
> to optimize bit more.
>
> I want to ask, is there any way to see the resulted *.tck (ROI tracking
> result) in 3D viewer. Just missing 3D feeling of track.
>
> Have a nice day
>
> best regards, vinod
>
>
>
> ----- Original Message ----
> From: Donald Tournier <d.tournier at brain.org.au>
> To: Kerstin Pannek <k.pannek1 at uq.edu.au>
> Cc: mrtrix discussion <mrtrix-discussion at www.nitrc.org>
> Sent: Thursday, September 4, 2008 4:25:59 AM
> Subject: Re: [Mrtrix-discussion] nii conversion and general questions
>
> 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
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


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