[Mrtrix-discussion] MRstats Specific to the Corticospinal Tract

[Donald Tournier]

Hi Kirles,

Luis is right that the TDI images shouldn't be regarded as quantitative at
this stage - hopefully we'll be able to come up with a more quantitative
variant in the future. That said, since you want to do these statistics,
there are many ways to solve your problem - assuming I understand it
correctly.

First off, I'm not sure why you want to use ImageJ at all for this. From
what you say, it sounds like what you're doing is thresholding the CST TDI
at a specific intensity and writing out a binary mask - this is what the MRtrix
'threshold' command<http://www.brain.org.au/software/mrtrix/commands/threshold.html>is
for. Besides, I have a vague recollection that the last time someone
here tried to use ImageJ, the image transform wasn't preserved so that the
images were no longer aligned in real space - not a huge problem since
mrstats doesn't use that information, and besides things may have changed
since then anyway.

The next thing is as Luis suggested, there is a -template option for
tracks2prob<http://www.brain.org.au/software/mrtrix/commands/tracks2prob.html>that
will produce a TDI in exact alignment with the template image
supplied. So you can generate your whole-brain TDI using:

$ tracks2prob tracks.tck -vox X TDI.mif


to get a high resolution image, and your ROI using:

$ tracks2prob CST.tck -template TDI.mif TDI_CST.mif


to guarantee alignment for use in mrstats, after having thresholded your
image to create a binary mask:

$ threshold TDI_CST.mif -abs N TDI_CST_mask.mif
$ mrstats TDI.mif -mask TDI_CST_mask.mif


Alternatively, you can regrid one image to match the other using the
mrtransform
command <http://www.brain.org.au/software/mrtrix/commands/mrtransform.html>,
again using the -template option. That said, the tracks2prob route is the
better option since it will avoid interpolation errors inherent in
regridding.

Hope that helps.
Cheers,

Donald.


On 6 July 2012 07:59, Luis Concha <lconcha at unam.mx> wrote:

> You can use
> tracks2prob -template TDI.mif CST.tck CST_p.mif
>
> However, it puzzles me that you want to extract statistics from
> (presumably) ultra-high resolution images. FA values should, in my opinion,
> be extracted from the original FA maps. On the other hand, it has been
> suggested that track densities are not something that is a quantifiable
> parameter for between-group analyses. I am hoping this opinion has changed
> and/or that some new way of analysis of TDI is available. Perhaps others
> can pitch in.
>
> Luis
>
>
>
> On Thu, Jul 5, 2012 at 4:39 PM, Kirles Bishay <kirles at ualberta.ca> wrote:
>
>> Hello,
>>
>> I am currently trying to get statistics specifically on the corticospinal
>> tract of my whole brain TDI images. So far, I have tried to create a mask
>> of just the CST to apply to the whole brain image by using the tractography
>> function in MRtrix, turning it into a TDI image, using ImageJ software
>> to convert the TDI image into a mask and then applying the mask back
>> in MRtrix to specify my ROI for the statistics function. While this works
>> well with the TDI image of just the CST, it does not work with the whole
>> brain image because the dimensions of the images are different. This is
>> because the dimensions created with my ROI tractography differ from the
>> dimensions of the whole brain tractography. I have tried to change the
>> dimensions of my mask image using ImageJ, but I think this warps the mask
>> inapropriately. Is there a way to control the output dimensions of the
>> tractography images so that I can match the CST mask to my TDI image? Or do
>> you have any other suggestions to get the data on the CST in my whole brain
>> images that I have not thought of?
>>
>> Thank you,
>>
>> Kirles
>>
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>>
>
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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