[slicer-users] Converting from DWI to DTI

Isaiah Norton inorton at partners.org
Wed Sep 15 15:49:36 EDT 2010


There is a module called "Resample DTI Volume" under 
Diffusion->Utilities with various interpolation types available.

On your original question of .nii.gz format: as far as I know, Slicer 
does not support writing tensor volumes as Nifti (nii). From a quick 
look, it seems like the underlying library (ITKNiftiImageIO) supports 
writing the necessary datatype NIFTI_INTENT_SYMMATRIX --so you could 
probably do  in tcl/python. Another route would be to reshape the raw 
file and build a header using fslcreatehd

More generally, if you are doing analysis in another program it will be 
easier to just converdirectly t nii from the original DICOM images if 
you have them (uing ie: mri_convert from FreeSurfer, dcm2nii, mricro/n, 
etc..).

-Isaiah

On 09/15/2010 03:13 PM, shoosh moosh wrote:
>
> Actually I needed it in that format in order to change its resolution 
> from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit 
> that requires the DTI volume to be in *.nii.gz.
> But can Slicer change the resolution without having to resort to that 
> tool? And if it does, does it do the interpolation, or does it simply 
> downsample?
> Thanks,
>
> ------------------------------------------------------------------------
> Subject: Re: [slicer-users] Converting from DWI to DTI
> From: demian at bwh.harvard.edu
> Date: Wed, 15 Sep 2010 16:00:27 -0300
> CC: slicer-users at bwh.harvard.edu; slicer-devel at bwh.harvard.edu
> To: babygirl_25 at hotmail.com
>
> Mmmmm
>
> that does not have an easy answer I guess. That export feature is not 
> yet implemented. What tools do you want to interact with?
>
> D
>
> --
> Demian Wassermann, PhD
> demian at bwh.harvard.edu <mailto:demian at bwh.harvard.edu>
> LMI / PNL / SPL Labs
> Harvard Medical School
> Brigham and Women's Hospital
> 1249 Boylston, Boston, MA, USA
>
> On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:
>
>     Great, thanks!
>     Now how do I convert from a DTI that is in (*.nhdr & *.raw.gz)
>     format to a DTI that is in *.nii.gz format?
>     Thanks
>
>
>     ------------------------------------------------------------------------
>     Subject: Re: [slicer-users] Converting from DWI to DTI
>     From: demian at bwh.harvard.edu <mailto:demian at bwh.harvard.edu>
>     Date: Wed, 15 Sep 2010 15:34:06 -0300
>     CC: slicer-users at bwh.harvard.edu
>     <mailto:slicer-users at bwh.ha%0A%20rvard.edu>;
>     slicer-devel at bwh.harvard.edu <mailto:slicer-devel at bwh.harvard.edu>
>     To: babygirl_25 at hotmail.com <mailto:babygirl_25 at hotmail.com>
>
>     Hi!
>
>     On the Diffusion menu -> Utilities there is one called Diffusion
>     Tensor Estimation.
>
>     You can find all the details regarding the process in:
>     http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionMRIWelcome-Documentation-3.6
>
>     Happy to help
>     Demian
>
>
>
>
>     --
>     Demian Wassermann, PhD
>     demian at bwh.harvard.edu <mailto:demian at bwh.harvard.edu>
>     LMI / PNL / SPL Labs
>     Harvard Medical School
>     Brigham and Women's Hospital
>     1249 Boylston, Boston, MA, USA
>
>     On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:
>
>         How do I convert from diffusion weighted image (*.nrrd format)
>         to Diffusion tensor image in slicer?
>         Thanks
>
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