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



 on behalf of Stephen Smith <<>>
Date: Friday, April 6, 2018 at 4:45 AM
To: Megan Ní Bhroin <<>>
Cc: "<>" 
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 

On 6 Apr 2018, at 10:41, Megan Ní Bhroin 
<<>> 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

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 file to my own environment for the ICA FIX bash script to run, is 
this correct?

Thank you for your time in advance.

HCP-Users mailing list<>

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)<>

Stop the cultural destruction of Tibet<>

HCP-Users mailing list<>

HCP-Users mailing list

Reply via email to