Hi Steve
Where do I upload files to?
Thanks
Jen
On Nov 27, 2007, at 1:21 AM, Steve Smith wrote:
> 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
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> ----
>
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