Hi - it seems pretty definite that you are trying to use non-valid
NIFTI files (which may have been ok with older versions because our
older code was less strict about NIFTI compliance but our latest code
uses the proper NIFTI sourceforge libraries). I would concentrate
first on sorting out the headers - if you need to upload an example
for us to look at, feel free.
Cheers, Steve.
On 26 Nov 2007, at 20:52, Jennifer Bramen wrote:
> I am having trouble scaling the intensities of my 3D volumes.
>
> I need to make sure the intensity ranges of my 3D volumes are about
> the same
> across subjects. In the past, I have had no trouble finding the
> intensity
> range of an image using avwstats -R, then multiplying the image using
> avwmaths so that all my 3Ds are about the same.
>
> Right now, I have a file which starts with a range of 0-200. If I
> use the
> following command in fsl 3.3:
>
> avwmaths Aud01_MPRAGE_corrected_susan -mul 10 Aud01_tst_v33_ic
>
> I correctly get an output with an intensity range of 0 -2000.
>
> If I do the same using the version 4.0 tools:
>
> fslmaths Aud01_MPRAGE_corrected_susan -mul 10 Aud01_tst_v4_ic
>
> I get an error
>
> "** WARNING: posn not header size (0, 348)"
>
> and I incorrectly get and image with a range of -21848.000000
> 31093.000000
>
> I ran correctheader. When I repeat the above fslmaths command on the
> fixed
> image, I get and output with an intensity range of -30704.000000
> 32342.000000
>
> I did the same test with a different image. I ran correctheader,
> then ran
> avwmaths/fslmaths -mul 2 and compared the outputs. The original file
> had an
> intensity range of 0-1000. The avwmaths (v 3.3) outfile had a range of
> 0.000000 2034.000000. The fslmaths (v 4.0) outfile had a range of
> -32768.000000 32512.000000 and gave an error of ** WARNING: posn
> not header
> size (0, 348).
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
|