[Camino-users] error when splitting tensor components with shredder

[Alessandro Calamuneri]

Hi Philip,
thanks for your reply! It worked the way you describe; I was indeed
wandering whether an easier way to split tensor components was available,
even if into tutorials this was the only way mentioned.
Would this approach work also for multitensors? I mean, if i fit a two
tensors model, knowing the storage is organized in that way

exitcodeEncodes information about the reconstruction procedure. -1 means
the voxel was skipped as background, 0 indicates success. Positive values
mean something went wrong in the reconstruction or some data was modified
or excluded. See
modelfit<http://cmic.cs.ucl.ac.uk/camino//index.php?n=Man.Modelfit>
for
details.lnA0Log of the geometric mean of all measurements at b=0 in this
voxel.numDTsNumber of Gaussian components in this voxel, from 0 to
N.mix_iMixing
fraction for tensor i, between 0 and 1. Sum of mix_i over all components is
1.d**_i

would the code

voxel2image -inputfile dt_2_tens.Bdouble -components 17
(=exitcode+lnA0+numDTs+mix_1+6*dt_1+mix_2+6*dt_2) ...

work?

The point is that I would like to warp all the components using flirt and
fnirt, and then go back to camino format with my warped data. How would in
this case work the multitensor reconstruction? Sorry but I do not know how
NIFTI multitensors are stored, than I do not have idea about what the
coding should be. Would nii2dt work also in this case?
Thanks in advance.

Best,
Alessandro



2014/1/23 Philip A Cook <cookpa at mail.med.upenn.edu>

> Perhaps the problem has to do with the ordering of the components. NIFTI
> tensors should be lower triangular (dxx, dxy, dyy, dxz, dyz, dzz).
>
> A simpler solution would be to use voxel2image:
>
>   voxel2image -inputfile dti.Bdouble -header image.nii.gz -components 8
> -outputroot dt_component_
>
> where image.nii.gz is an image with the correct header information (such
> as the raw DWI data).
>
> The above gives you the components. If you want the tensor in NIFTI
> symmatrix format, you can use dt2nii.
>
>
> On Jan 23, 2014, at 10:28 AM, Alessandro Calamuneri <
> alecalamuneri at gmail.com> wrote:
>
> > Hi all,
> > I would like to obtain tensor components computed with using modelfit
> and nldt_pos as algorithm. Everything seems to work properly, as I can also
> correctly visualize results using e.g. pdview.
> > But when I want to split this file to obtain single components I eot
> stuck: here is my code
> >
> > for  ((i=0;i<8;i=i+1));do
> > #splitting tensor into its components
> > shredder $((i*8)) 8 56 < dti.Bdouble > DT_comp${i}.img
> > #creating proper header
> > analyzeheader -voxeldims 1.75 1.75 2 -datadims 128 128 74 -datatype
> double > DT_comp${i}.hdr
> > done
> >
> > If I have correclty understood,my output should be
> >
> > DT_comp0.img which contains exitcode
> > DT_comp1.img which contains log of unweighted signal
> > DT_comp2.img which is DT_xx
> > DT_comp3.img which is DT_xy
> > DT_comp4.img which is DT_xz
> > DT_comp5.img which is DT_yy
> > DT_comp6.img which is DT_yz
> > DT_comp7.img which is DT_zz
> >
> > Now, to check if my assumptions are correct I go back to tensor by means
> of nii2dt function (before doing that I merge volumes using fslmerge)
> >
> > fslmerge -t tensor DT_xx.nii DT_xy.nii DT_xz.nii DT_yy.nii DT_yz.nii
> DT_zz.nii
> >
> > so
> >
> > nii2dt -inputfile tensor.nii.gz > dt.Bdouble
> >
> > eventually I calculate fa
> >
> > cat dt.Bdouble | fa | voxel2image -outputroot my_fa -header tensor.nii.gz
> >
> > But when I look at the results fa map is totally wrong as the fa values
> are in the range [.9 1.2], which is impossible of course.
> >
> > I also tried using linear option and addingo lns0 and mask (inverting
> endianness as described for mask output of bet2 function) as well .In this
> last case the code was
> >
> > nii2dt -inputfile tensore.nii.gz -bgmask mask.img -lns0 DT_comp1.img >
> dt.Bdouble
> >
> > but with no amelioration at all.
> >
> > Where am I wrong? Is the position of tensor components wrong?
> > Is the reconstruction back to camino tensor wrong?
> > Is shredder badly used?
> > Is it a problem of mask endianness?
> >
> >
> > Hope you can help me,
> >
> > Best,
> > Alessandro
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
>
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