Hi,
Yes, you need to specify the percentage threshold for the
background. Normally a value of 10 (as in 10%) works well.
So try running:
$FSLDIR/bin/ip I/Pfile O/Pfile 10 -t hp_value lp_value
All the best,
Mark
On 18 Oct 2005, at 22:07, Shruthi Chakrapani wrote:
> Hello
>
> I am trying to do Temporal bandpass filtering using the ip command on
> the
> output of BET(.img).I am not sure what I am doing is right.I know that
> the
> values for highpass and lowpass are to be specified in volumes and not
> in
> seconds.The exact command line I am running is something like this
>
> ip I/Pfile O/Pfile -t hp_value lp_value
>
> where "value" is the numbers I plug in.
>
> When I run this command it just prints out this....
>
> Usage: /usr/pubsw/packages/fsl/current/bin/ip_16SI <DEFANGED_input>
> <output>
> <%threshold> [options]
>
> -s <sigma> : spatial lowpass Gaussian linear filtering (sigma in mm,
> not voxels)
> -S <width> : spatial lowpass median filtering (width is full cube
> width in
> voxels)
> -m <mask_filename> : create binary mask, apply to fmri data and save
> mask to
> file
> -i <target mean> : global intensity normalisation (separate intensity
> rescaling for each 3D volume)
> -I <target mean> : grand mean intensity normalisation (one intensity
> scaling
> for the whole 4D data set)
> -t <hp_sigma> <lp_sigma> : Bandpass temporal filtering; nonlinear
> highpass
> and Gaussian linear lowpass (with sigmas in volumes, not seconds); set
> either sigma<0 to skip that filter
> -T <hp_sigma> <lp_sigma> : Same as -t, but only uses previous
> timepoints wrt
> each timepoint for filtering
>
>
> I am not sure what is going wrong.Does anyone know what to do?
>
> Thanks
> Shru
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