The output will be named
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean.dtseries.nii.
You will need to look into the logs more deeply than that. I would guess
there is an issue with your installation of R and its package dependencies.
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Joey Contreras
<joey.contre...@loni.usc.edu<mailto:joey.contre...@loni.usc.edu>>
Date: Thursday, November 2, 2017 at 3:36 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] difference between fix and hcp-fix (ICA+FIX scripts) and
outputted files
Hello
I wanted to get some further clarification on the ICA+FIX pipeline
Within the fix directory I used the command:
>>hcp_fix
>>/sourcedir/subject/MNINonLinear/Results/rfMRI_REST_AP/rfMRI_REST_AP.nii.gz
>>2000
processing FMRI file rfMRI_REST_AP with highpass 2000
running highpass
running MELODIC
running FIX
FIX Feature extraction for Melodic output directory: rfMRI_REST_AP_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: rfMRI_REST_AP_hp2000.ica using
training file:
/ifs/loni/faculty/jpa/4Joey/PPG_fc/scripts/fix1.065/training_files/HCP_hp2000.RData
and threshold 10
No valid labelling file specified
1. Given the following output "No valid labelling file specified” were can I
specify this file?
2. What is the difference between running fix and hcp_fix
3. Is there documentation on all the outputted files from the script? (i.e. an
atlas.dtseries.nii file was generated in the rfMRI_REST_AP_hp2000.ica created
folder. Would this be the new cleaned 4D data)? Essentially I am looking for my
cleaned 4D resting state data to be able to obtain correlation matrices for
this cleaned data
Any help/clarification with these questions would be appreciated
Thank you!
Joey Contreras
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