[Mrtrix-discussion] track_info and normalise_tracks

[Donald Tournier]

Hi Markus,

1) >> track_info
>
> is it possible read the count value into a variable? I tried with awk,
> like I do with some fsl functions:
>
> track_info_output=`track_info L_SubstInn_CapsExt_tract.tck`
> cout=`echo $count | awk '{print $1}'`
>
> I take $1 because it is in the first line of the output.
>
> However, I am puzzled to find the whole directory content in the $count.
>

This works for me:
count=`track_info mytrack.tck | grep '\<count:' | awk '{ print $2 }'`


> 2) >> normalise_tracks
>
> What type of warp image is needed here? I cannot find any specifications
> (the ideal would be to feed in the warps created by the fsl TBSS pipeline.
> Is there any hope?)
>

Indeed, not a lot of information on this anywhere... It's the simplest
thing I could think of: it's a 4D file (3 volumes), with each voxel
reporting the coordinates of the position it maps to in the other space.

The idea behind that choice, besides simplicity, is to allow extraction of
the warp field regardless of the normalisation package used - they all
store the transformation information in different ways, so it's impossible
to support them all directly. Essentially, it works by generating a 'no
warp' image, simply by taking a given image and assigning to each voxel its
own location in real/scanner coordinates - this is what gen_unit_warp does.
Since this is a just like any other image, you can then use whichever
package you used to estimate the warp (SPM, ANTS, FNIRT, etc) to apply the
warp to the 'no-warp' image. The resulting warped image contains the
required warp information, in the format expected by normalise_tracks: each
voxel reports its original position.

For more information, there is an entry about it in the FAQ:
http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks

Cheers,

Donald.



> Thanks again and best wishes!
> Markus
>
>
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>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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