Please upload the files in a single compressed tarfile to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
And then email me the upload ID.
On 27 Nov 2007, at 17:53, Jennifer Bramen wrote:
> 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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---------------------------------------------------------------------------
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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