How about the BXH/XCEDE tools? They were developed by Syam Gadde here at
Duke, and they are excellent for jumping around between image types.
http://www-calit2.nbirn.net/tools/bxh_tools/index.shtm
You can use bxhabsorb to fit the data with a bxh header, and then
bxh2analyze to convert from nifti to analyze. There are a bunch of options
that you can look at to check orientation as well!
Best,
Vanessa
On Mon, Nov 8, 2010 at 2:19 PM, Matthew Brett <[log in to unmask]>wrote:
> Hi,
>
> > Our lab here has an in house software package that only reads analyze
> images. I'm trying to do some reorientation and registration in SPM5/8, but
> I need to then convert to analyze hdr/img pair and write out the image in
> the new orientation. I've tried a few programs, but they all also generate
> the *.mat file needed by older versions of SPM to store the orientation.
> What I really need is something that will take a nii format file and write
> out an analyze format file where the the image volume is actually physically
> written in the correct orientation.
>
> If the .mat file only encodes some axis flips or axis rearrangements,
> then you could try our 'nibabel' python package [1]:
>
> easy_install nibabel
> python
> >>> import nibabel as nib
> >>> img = nib.load('nifti_image.nii')
> >>> better_img = nib.as_closest_canonical(img)
> >>> nib.analyze.save(img, 'better_analyze_image.img')
>
> By the way - this will generate a 'neurological' orientation image
> (first pixel is the right-most pixel).
>
> If there are rotations and translations so that the image does not
> align down any reorganization of the axes, you'll have to reslice the
> image to some canonical volume...
>
> Best,
>
> Matthew
>
> [1] http://nipy.sourceforge.net/nibabel/
>
--
Vanessa Villamia Sochat
Laboratory of Neurogenetics
Duke University, 2009
(603) 321-0676
