[Camino-users] tensor format and get tensor components

[xiaoping qu]

Hi Philip,

Thanks for your reply  and it is really helpful.
I have use split4dnii to split NIFTI format tensor to 6 components (lower
triangle), and they are automatically named as

0001.nii.gz  0002.nii.gz  0003.nii.gz  0004.nii.gz  0005.nii.gz
0006.nii.gz.


To use DTITK function to fit tensor, I need to know the what the number
represent.


Does 0001 represent dxx,

     0002 represent dxx,

     0003 represent day,

     0004 represent dzx,

     0005 represent dzy,

     0006 represent dzz ?


The meaning for the tensor components is very important for me to do next
process.


Thanks for your patience and help,

Xiaoping




2016-08-05 15:17 GMT-07:00 Philip A Cook <cookpa at mail.med.upenn.edu>:

> Hi,
>
> 1. Camino's raw data format is upper triangular, but dt2nii will write
> tensors with lower triangular elements, as specified by NIFTI. These should
> work with DTI-TK. You will have to do other pre-processing, see the DTI-TK
> documentation here
>
> http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.BeforeReg
>
>
>
> 2. If you want the components back you can call split4dnii, which will
> split 4D or 5D nii into 3D images.
>
>
> 3. I don't recommend using analyzedti or any Analyze files, they are
> obsolete now. With NIFTI:
>
> dtfit data.nii.gz mask.nii.gz | dt2nii -header mask.nii.gz -outputroot
> myDT_
>
> This will make
>
> myDT_dt.nii.gz
> myDT_exitcode.nii.gz
> myDT_lnS0.nii.gz
>
> You can then do
>
> fa -inputfile myDT_dt.nii.gz -outputfile myDT_fa.nii.gz
> md -inputfile myDT_dt.nii.gz -outputfile myDT_md.nii.gz
>
> If you want the full eigen system, things are a little trickier, but you
> can use voxel2image to get the output of dteig as a series of NIFTI images
> (see http://camino.cs.ucl.ac.uk/index.php?n=Main.Fileformats). It would
> be nice to have a dteig2nii to automate this, but we don't currently have
> that.
>
> If you are using DTI-TK, then you can take the NIFTI DT and use it's
> TVTool to get the eigen system, as well as AD, RD, MD, FA, etc.
>
>
>
>
> > On Aug 5, 2016, at 5:33 PM, xiaoping qu <quxiaoping1 at gmail.com> wrote:
> >
> > Hi Camino experts,
> >
> > I am Xiaoping, a new user to Camino.
> >
> > Since I want the diffusion tensor  components to do registration with
> DTITK, I am very interested in tensor type and how to abstract tensor
> components from a tensor file.
> >
> > 1. I tried to use dtfit to fit a tensor with Bdouble format and can use
> dt2nii to convert Bdouble format file to nifti format.
> > According your on line documents, I find that the tensor.Bdouble from
> dtfit is upper triangle but no idea about the nifti tensor format?
> > Can you tell me  that after dt2nii, what type the nifty format tensor is
> ? upper triangle or lower triangular?
> >
> >
> > 2. If I want to extract tensor components like dxx, dxy, dxz, dyy, dzz
> from tensor.nii.gz, what kind of function I can use?
> >
> >
> >
> > 3. Aso, according to the online documents about camino, I just find
> analyzedti is a command to get individual analyze format components. If I
> have the DWI nifti.gz format image and its binary mask(nii,gz) and scheme
> file. How can I use analyzedti to get individual tensor components?
> >
> > Do I need to fist img2voxel to convert dwi to voxel order as Bfloat file,
> > and then use voxel2scanner to convert dwi.Bfloat to scanner order as
> Bdouble file, and then use AnalyzeHeader to convert Bdouble to analyze
> format, and finally use Analyzedti to get analyze format tensor components?
> >
> >
> >
> > Thanks,
> > Xiaoping
> > _______________________________________________
> > Camino-users mailing list
> > Camino-users at www.nitrc.org
> > http://www.nitrc.org/mailman/listinfo/camino-users
>
>
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