He Leah,
It should not be necessary for you to change any of the lines you show
below from the FIX settings.sh file.
Of course, there are certainly lines after those lines in sections
labeled "Part I MATLAB settings", "Part II Octave settings", and "Part
III General Settings" that you will need to review and update to reflect
your environment. But I believe that the lines you have copied into your
email should be fine "as is".
Tim
On 11/02/2017 04:28 PM, Marta Moreno wrote:
Dear experts,
I want to use the “hcp_fix" script for clean up of resting state data
after HCP pipelines. I am editing “settings.sh" and wanted to know if
I have to edit these lines copied below:
# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
# (actually this version is 1.065 - see wiki page for details)
# Get the OS and CPU type
FSL_FIX_OS=`uname -s`
FSL_FIX_ARCH=`uname -m`
if [ -z "${FSL_FIXDIR}" ]; then
FSL_FIXDIR=$( cd $(dirname $0) ; pwd)
export FSL_FIXDIR
fi
Thank you very much,
Leah
On Oct 30, 2017, at 10:29 AM, Marta Moreno <mmorenoort...@icloud.com
<mailto:mmorenoort...@icloud.com>> wrote:
Great. Thank you very much.
On Oct 29, 2017, at 4:44 PM, Glasser, Matthew <glass...@wustl.edu
<mailto:glass...@wustl.edu>> wrote:
Yes that is what we do.
Peace,
Matt.
From: Marta Moreno <mmorenoort...@icloud.com
<mailto:mmorenoort...@icloud.com>>
Date: Sunday, October 29, 2017 at 12:03 PM
To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>>
Cc: HCP Users <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA+FIX cleanup scripts
Thanks for your answer. I just want to use the “hcp_fix" script
for clean up of resting state data after HCP pipelines. I only need
to know if I just need to run the “hcp_fix" on data already
preprocessed with HCP pipelines, after which I get my clean
dtseries.nii ready for FC analyses.
Much appreciation.
<Signature.png>
On Oct 29, 2017, at 11:41 AM, Glasser, Matthew <glass...@wustl.edu
<mailto:glass...@wustl.edu>> wrote:
I think there is a readme with instructions on set up. If you have
specific questions about those, ICA+FIX questions might be best
asked on the FSL list, as the FSL programmers don’t watch this
list. Here we can answer questions about CIFTI or approaching
clean up of resting state data.
Peace,
Matt.
From: <hcp-users-boun...@humanconnectome.org
<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta
Moreno <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>>
Date: Sunday, October 29, 2017 at 9:11 AM
To: HCP Users <hcp-users@humanconnectome.org
<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] ICA+FIX cleanup scripts
Dear experts,
I would like to use ICA+FIX cleanup after HCP minimal preprocessing
pipelines on high quality resting-state data acquired with a GE
scanner. HCP minimal preprocessing is working fine and installed
locally. I have downloaded now the tar file with ICA+FIX cleanup
scripts. Could you please give me some guidelines on what are the
steps to follow to have them running? I am using a MacPro.
Much appreciation for your help.
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/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Connectome Coordination Facility)
tbbrown(at)wustl.edu
/
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