[SciPy-dev] Nifti support

John Ollinger ollinger@wisc....
Thu Oct 4 16:28:54 CDT 2007


Hi,

It should read DTI images, but I have only tested it on GE scanners.  The
code does support Siemens scanners, so it wouldn't take much to get it to
work.

I did not wrap FSL or SPM.  I am not sure how to wrap programs written in
matlab.  Other than to use matlab itself.

The code return a 4x4 transformation matrix that takes the raw data into RAI
coordinates.  It doesn't do anything to the data itself.

I will put the code and some documentation (yet to be written) on my home
page, probably tomorrow but maybe Saturday.

John


On 10/4/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
>
> Hi,
>
> Here is the nifticlib.i file, not a lot of differences.
>
>
> I would like to put in my two-cents worth regarding the nifti format.  I
> > wrote a library in python that handles dicom, afni, and nifti format with
> > the appropriate conversions between coordinate systems.
>
>
>
> Are you able to read DTI image files in DICOM ? That could interest me a
> lot.
>
>
> The goal was to be able to script FSL, AFNI, SPM and our in-house python
> > code without doing a file conversion at every step.
>
>
>
> Do you have a wrapper over FSL and SPM in Python ?
>
>
> Unfortunately,  AFNI defines the quaternion transformation relative to LPI
> > coordinates, while FSL defines it as going to RAI.  I don't know how SPM
> > does it - we are still in the process of scripting that.   The result is
> > that either the fans of fslview or the fans of AFNI are upset about any
> > given solution.
>
>
> We have the same problem when converting DICOM to analyze, the two pieces
> of software we use (MRIConvert and MRICRO or something like that) don't use
> the same coordinate system...
>
>
> I don't know if this is covered elsewhere or not, but it should receive
> > some attention.
> >
>
> You have mine :)
>
> Matthieu
>
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>
>


-- 
John Ollinger
University of Wisconsin
Waisman Center, T233
1500 Highland Ave
Madison, WI 53711
http://brainimaging.waisman.wisc.edu/~jjo/
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