Hi Kelly - you really need to use tbss_1_preproc. The IRKT nonlinear
reg software requires the datatype that tbss_1_preproc outputs, which
includes being integer format - that's why (eg) float values in the
range 0:1 are scaled up by default to 0:10000 integers - hence it
doesn't matter that the output is not float as sufficient decimal
places are in effect kept.
Hope this helps, Steve.
On 16 Mar 2007, at 19:04, Kelly wrote:
> Hi,
>
> Can you please help me to understand the commands tbss_1_preproc uses
> to convert nifti files into analyze format for input into nreg? I
> would like to convert my files while keeping the native data type
> (i.e.
> not rounding to the nearest integer which is what the tbss_1_preproc
> script does) but simply using:
> export FSLOUTPUTTYPE=ANALYZE
> and then multiplying by the necessary factor
> ($FSLDIR/bin/avwmaths++ $f -mul $FACTOR ${BDIR}/${f}_conv -odt double)
> does not work. I receive an error when inputing into nreg. However, if
> I change the file to analyze manually via FSLview (by saving as:
> *.hdr)
> and then multiply by the factor the format will be accepted without
> error by nreg and I can keep my native voxel values. Can you please
> tell me what fslview is doing differently than the tbss_1_preproc
> script of:
>
> $FSLDIR/bin/avwhd -x $f | sed "s/sform_code .*/sform_code = \'0\'/g" |
> sed "s/qform_code .*/qform_code = \'0\'/g" > grot.xml
> $FSLDIR/bin/avwcreatehd grot.xml FAi/${f}_FAi.hdr
> /bin/rm grot.xml
>
> so I that I can change my script accordingly? Thanks so much!
>
> Kelly Brown
>
> $FSLDIR/bin/avwmaths_16SI FAi/${f}_FAi -ero FAi/${f}_FAi
>
>
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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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