[Mrtrix-discussion] voxel size and useless black image slices

[Donald Tournier]

Hi Eric,

The last voxel size is undefined - it's along the 4th (volume) axis, so is
essentially unit-less anyway. This is why it's labelled with a '?'.

The reason why the slices keep going without stopping in MRView is because
you might be displaying other things (e.g. tracks) generated from other
images with a larger FOV than what you're currently showing as the main
image. For this reason, MRView doesn't stop you from going outside the FoV.

As to the problem with black slices inside the dataset, this suggest there
might be issues with your DICOM data - or at least with MRtrix's
interpretation of them. As a first attempt, maybe you could post the output
of the following commands:

$ mrconvert -debug your_DICOM_folder dwi.mif
$ mrinfo dwi.mif

You may want to edit these output to remove any patient-sensitive
information if needed. Alternatively, you can send me these outputs
privately in whichever way you feel is sufficiently secure.

If that doesn't provide enough information, it might be easiest if you
could send me the data so I can have a close look at what is going wrong,
but let's try with the above first.

Cheers,
Donald.



On Thu, Jun 19, 2014 at 5:30 AM, Qiang Yu <yoh_ren at 126.com> wrote:

> Dear all,
>
> I'm new using MRtrix, therefore I'm following the online manual in order
> to understanding this software. However, after I imported DWI data, I found
> that voxel size is " 1.549*1.549*1.5*?" , where the last number is ? that
> is very stranage. In addition, I used command: mrview dwi.mif to see the
> image, and I found that the image slices keep going and never stop, and
> many useless black image slices inside. I don't know how to fix it? Does
> someone could give me some suggestions?
>
> Many thanks.
>
> Regards,
> Eric
>
>
>
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>


-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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