Hi Mark
Thanks I guess it worked....
Shru
On Tuesday, October 18, 2005, at 05:28 PM, Mark Jenkinson wrote:
> 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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