Hi - I would think the easiest and best thing to do would be just to apply more 
aggressive high-pass filtering to the already FIX-cleaned data.
Was there a reason you didn't want to do that?   It's not at all a problem that 
the less aggressive HP filter had already been applied before original FIX 
cleaning.
Cheers.


> On 6 Apr 2018, at 10:41, Megan Ní Bhroin <nibhr...@tcd.ie> wrote:
> 
> Hi there, 
> 
> I'm very new to Neuroimaging but wondering if you could help me with some 
> issues I am having. 
> 
> I want to run the ICA FIX pipeline on HCP resting state data. I wish to do 
> this as I would like to apply a more aggressive temporal filtering than is 
> already in place. 
> 
> Do you have any suggestions on how to alter the script, the code already in 
> place has a cut off of 2000s but I wish to apply a high pass temporal filter 
> of 69.444 and low pass temporal filter of 0.7716.
> 
> echo "processing FMRI file $fmri with highpass $hp"
> 
> if [ $hp -gt 0 ] ; then
>   echo "running highpass"
>   hptr=`echo "10 k $hp 2 / $tr / p" | dc -`
>   ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 ${fmri}_hp$hp
>   fmri=${fmri}_hp$hp
> fi
> 
> 
> I believe the correct data to run this script on is Resting State fMRI 1 & 2 
> Preprocessed, can you point me towards the exact files to run this on?
> 
> For this script to run successfully I believe that I first have to modify the 
> settings.sh file to my own environment for the ICA FIX bash script to run, is 
> this correct?
> 
> Thank you for your time in advance.
> Best, 
> Megan
> 
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.uk    http://www.fmrib.ox.ac.uk/~steve 
<http://www.fmrib.ox.ac.uk/~steve>
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