Also why do you need to do this to begin with?

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Stephen Smith <st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>>
Date: Friday, April 6, 2018 at 4:45 AM
To: Megan Ní Bhroin <nibhr...@tcd.ie<mailto:nibhr...@tcd.ie>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA-FIX

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<mailto: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









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Head of Analysis,  Oxford University FMRIB Centre

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st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>    
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