Hi, this is the following lines of TCL:
if { $fmri(smooth) > 0.01 } {
set smoothsigma [ expr $fmri(smooth) / 2.355 ]
set susan_int [ expr ( $median_intensity - $int2 ) * 0.75 ]
fsl:exec "${FSLDIR}/bin/fslmaths $funcdata -Tmean mean_func"
fsl:exec "${FSLDIR}/bin/susan $funcdata $susan_int $smoothsigma 3
1 1 mean_func $susan_int prefiltered_func_data_smooth"
fsl:exec "${FSLDIR}/bin/fslmaths prefiltered_func_data_smooth -
mas mask prefiltered_func_data_smooth"
set funcdata prefiltered_func_data_smooth
set ps "$ps; spatial smoothing using a Gaussian kernel of FWHM
$fmri(smooth)mm"
}
set normmean 10000
if { $fmri(norm_yn)} {
fsl:exec "${FSLDIR}/bin/fslmaths $funcdata -inm $normmean
prefiltered_func_data_intnorm"
set ps "$ps; multiplicative mean intensity normalization of the
volume at each timepoint"
} else {
set scaling [ expr $normmean / $median_intensity ]
fsl:exec "${FSLDIR}/bin/fslmaths $funcdata -mul $scaling
prefiltered_func_data_intnorm"
set ps "$ps; grand-mean intensity normalisation of the entire 4D
dataset by a single multiplicative factor"
}
set funcdata prefiltered_func_data_intnorm
so the 888.96945225 comes from the median intensity in the brain minus
the 2nd percentile,
2.12314225053 is the spatial kernel size (sigma) in the SUSAN
smoothing
and 8.43673534677 is the intensity scaling factor applied to the whole
4D dataset so that its mean is then 10000
Cheers.
On 16 Apr 2010, at 17:50, Lejian Huang wrote:
> Hi Mark,
>
> In the FSL Archive (025336, 025386, and 025420), Nick asked a
> question about how to generate several argument numbers in prestats
> command lines. Unfortunately, it is unanswered.
>
> Here is my part of the Prestats Report after using GUI:
>
> usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean
> mean_func
>
> /usr/local/fsl/bin/susan prefiltered_func_data_thresh 888.96945225
> 2.12314225053 3 1 1 mean_func 888.96945225
> prefiltered_func_data_smooth
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask
> prefiltered_func_data_smooth
>
> /usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul
> 8.43673534677 prefiltered_func_data_intnorm
>
>
> I'm wondering if you could tell me how to generate 888.96945225,
> 2.12314225053, and 8.43673534677 ?
>
> Thanks,
>
> Lejian
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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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