[Mrtrix-discussion] transform and normalise tracks

[Donald Tournier]

Hi Ping,

I'm guessing your issues are due to the fact that ANALYZE does not store the
transformation matrix (i.e. the directions of the axes and location of the
origin with respect to real/scanner space), whereas NIfTI does. This is one
of the reasons I urge everyone to stay well away from ANALYZE format images
(the other being that left/right ordering is ill-defined).

If you convert a NIfTI image with a proper transformation matrix to ANALYZE,
that information is lost. I guess the overlay function in FSLView operates
on a voxel-by-voxel basis - i.e. that the transformation information is
ignored, and only voxel coordinates within the imaging volume are taken into
account. This is not the case for MRtrix: each voxel is displayed in the
correct location, according both to its voxel coordinate within the imaging
volume, and the transformation information. Note that with ANALYZE images,
MRtrix will insert a default identity transform (no rotation, origin in the
middle of the dataset). That should explain the mismatch in the overlay. If
you want to double-check this, use 'mrinfo' on both images, and see if the
transforms differ.

On the other hand, I have no idea why the TDI maps are so different. I'm
assuming you have to supply your own gradient encoding, and that you're
using the same encoding file in both cases? Other than strange effects due
to different gradient encodings, I have no idea what the issue might be. One
possibility is that you're using a gradient table suitable for analysis
using FSL, where the gradient directions are supplied with respect to the
image axes. Since MRtrix assumes that they are supplied with respect to
real/scanner space, if there is a significant rotation component in the
transformation, the tracking will be affected. Might explain why the
tracking is OK with ANALYZE (the transform has been discarded - no rotation)
but not with NIfTI. Although there doesn't seem to be a huge rotation
between them judging from your screenshot...

On a final note, if you have access to the DICOM data, why not use MRtrix to
do the conversion for you? If you convert to MRtrix image format (.mif), you
will have the correct transform information, the DW gradient table will be
inserted in the header, and you shouldn't have any problems of this kind.

Hope that sort things out for you.
Cheers,

Donald.


On 12 January 2011 15:24, Ping-Hong Yeh <pinghongyeh at gmail.com> wrote:

> 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
> >
>



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