Hi Steve,
I did. The procedure I followed was as follows (I was working from the
command line).
/betfunc {file}.hdr b{file} %Where {file} has already been preprocessed by
other means (motion correction, smoothing, normalization, etc.)
/ip b{file}.hdr fb{file} 10 -s 1.273 -t 100.0 -1
/melodic -i fb{file}.hdr -o fb{file}.ica -v -bgthreshold=10 --tr=1
-mmthresh=0.5 --report --0all %Where fb{file} is the filtered, brain
extracted, preprocessed file
I then use the filter option as described below with the fb{file}.hdr file
as input and filtered_fb{file}.ica as output with the appropriate components
to be filtered. I expected for the filtered_fb{file}.img to simply be a
recomposition from the mixing matrix minus the selected components, but when
I perform melodic on the filter output file I get many more components than
I thought I would. Is this because there is unaccounted for variation
during the original ICA operation that is now coming into play?
Thanks for your help!
Tim
On Mon, 19 Mar 2007 15:10:50 +0000, Steve Smith <[log in to unmask]> wrote:
>Hi,
>
>Did you apply the cleanup to the data after it had been through the
>other preprocessing steps (motion correction etc.)?
>
>If you used the Melodic GUI then there should be a file called
>filtered_func_data in the original .ica output directory, and you
>should be feeding THAT preprocessed image into the cleanup.
>
>Does this help resolve things?
>
>Cheers, Steve.
>
>
>
>
>On 15 Mar 2007, at 15:12, Timothy Laumann wrote:
>
>> Dear FSLlist,
>>
>> I have been trying to use the filter option to remove noise from my
>> data and
>> I am wondering how exactly the function works. I thought that the
>> filter
>> function was merely removing the specified components from the
>> mixing matrix
>> and rebuilding the data sans those components. Just to see what would
>> happen, I filtered 25 of the 50 components generated from a 200
>> image dataset,
>>
>> melodic -i data.hdr -v -o filtered_data.ica --mix=melodic_mix -f
>> "2,3,.."
>>
>> and then performed a melodic ICA on the filtered_data.img that is
>> created.
>> I expected to get the 25 remaining components only, but instead
>> still got
>> close to 50 components. Clearly there is something about this
>> process that
>> I do not understand.
>> Thanks for the help!
>>
>> Tim
>
>
>------------------------------------------------------------------------
>---
>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
>------------------------------------------------------------------------
>---
>=========================================================================
