The precise process in the FIX pipelines is hopefully clear upon reviewing
 (including the FIX subfunctions that it calls).

If you started from a different starting point than the hcp_fix script, there 
are a few candidate reasons why your results might not match the released FIX 
- read in different motion parameter file
- did not use 2000s highpass filter on data and on motion parameters
- ran your own MELODIC, instead of using the MELODIC ICA output in the FIX 
extended packages (I believe that the FIX scripts re-run / overwrite MELODIC by 

If these don’t seem to be the issue, it might help to know a bit more about how 
the two outputs actually differ. (e.g., Is the difference within machine 


Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864

> On Sep 16, 2016, at 12:17 PM, Ely, Benjamin <> wrote:
> Hi all,
> I ran a test recently comparing "aggressive" vs. "soft" denoising in MELODIC 
> on an HCP resting-state run, regressing out the "bad" components found in the 
> rfMRI_REST1_LR_hp2000.ica/.fix file (I believe the location of this info is 
> different in the newer release but I'm working off HCP500 data). Both 
> denoising methods gave similar results which also looked similar to the 
> released HCP ICA-FIX denoised timeseries (i.e. 
> rfMRI_REST1_LR_hp2000_clean.nii.gz), but I expected the soft denoised MELODIC 
> output to be identical, which it was not. Is there a step I'm missing, or did 
> you run the ICA component regression with a different tool?
> Thank you!
> -Ely
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