[Mrtrix-discussion] transform and normalise tracks

[Ping-Hong Yeh]

Hi Donald,

 Thank you for the detailed explanation.

Another question about the input data format.

First, I have the same DWI data saved as NIFTI or ANALYZE. The  NIFTI
was converted from DICOM originally using dcm2nii and then to ANALYZE
using FSL fslchfiletype. Both images are aligned well while viewing
using FSLview (see attached  Screenshot_fslview.png); but there is a
significant translation while viewing using mrview
(mrview_screen.jpg).

I then processed both data and created the whole brain TDI images, but
the results are quite different (see tdi_analyze.jpg and
tdi_nifti.jpg).  It appear the TDI image by using ANALYZE is what TDI
is supposed to be looked like although now it does not align with
original NIFTI data, which has made the previous co-registration
matrices useless.


Thank you,

Ping


On Mon, Jan 10, 2011 at 8:14 AM, Donald Tournier
<d.tournier at brain.org.au> wrote:
> Hi Ping,
> Unfortunately, the 'normalise_tracks' command can't be used to apply a 4x4
> affine transform: it's designed to apply a non-linear warp to the track
> data. The warp information should be supplied as a 4D image, where the
> values for each voxel are set to the coordinates that this voxel maps to. To
> help generate the warp, there is a utility called 'gen_unit_warp', which
> will generate a 'no warp' image (i.e. each voxel contains its own location),
> to which you can apply the relevant inverse warp using whatever software
> package you use for your normalisation (FSL, SPM, etc). You can then feed
> the result to 'normalise_tracks' as the transform image.
> Getting the details can be quite tricky, so here is an example using SPM8,
> using the warp computed by normalising a T1 image (anat.nii) previously
> coregistered with the FA:
> Assuming you are normlising to the default T1 template image (T1.nii)
> supplied with SPM8, start by generating a unit warp image using that as a
> template:
> $ gen_unit_warp /opt/SPM8/templates/T1.nii warp-[].nii
> Note that the output image has been specified as a multi-file NIfTI, so this
> should produce the files warp-1.nii, warp-2.nii & warp-3.nii.
> Then estimate the warp you're interested in applying. In SPM8, select
> SPM->Spatial->Normalise->Estimate in the batch editor, specify the anat.nii
> as the source image, and T1.nii as the template, and run. This will generate
> the warp information as a "anat_sn.mat" file.
> Then, apply the inverse warp to your warp-*.nii images: select
> SPM->Util->Deformations in the batch editor, choose "New: inverse" as the
> composition, then "New: Imported _sn.mat" as its composition, "anat_sn.mat"
> as the parameter file, and your fa.nii as the "image to base inverse on".
> Specify all 3 wrap-*.nii in the "apply to" field, and run.
> This should generate 3 new files: wwarp-*.nii, which can be used directly in
> "normalise_tracks":
> $ normalise_tracks tracks.tck wwarp-[].nii tracks_normalised.tck
> Obviously the steps would be very different depending on the normalisation
> package you're using, but the idea would be the same.
> Hope that clarifies things a little.
> Cheers,
> Donald.
>
> On 7 January 2011 15:47, Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:
>>
>> Hello all,
>>
>>  I would like to transforming the tracks to the template space, but
>> not sure how to apply the transformation matrix (4 by4 Ascii) using
>> "normalise_tracks".
>> How should the normalisation map be created?   Thanks.
>>
>> Ping
>> _______________________________________________
>> 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
>
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