We didn’t create the HCP Pipeline BIDS app, and have no experience using it.  
Users should be aware that the current BIDS App “hides” various choices that 
one would normally have to make when running the HCP Pipelines, and I’m not 
sure what particular choices it has implemented.  In that regard, starting with 
the BID App, rather than the HCP Pipeline scripts themselves, may abstract the 
pipelines in a manner that is not conducive to you understanding what they are 
doing with your data.

Additionally, last time I checked (which was many months ago) there was no 
simple process for getting HCP-style acquired data into the BID directory 

More fundamentally, the “PEpolar” method for correcting the distortions expects 
that spin-echo acquisitions with both polarities were collected, so that you 
avoid susceptibility dropout and can estimate the field properly throughout the 
entire brain.  The HCP Pipelines are not constructed to correct for distortions 
using gradient-echo acquisitions to estimate the field maps, and thus I rather 
doubt that the BIDS app is equipped to handle that situation either, since the 
BIDS app is simply a “wrapper” into the HCP Pipeline scripts.


Michael Harms, Ph.D.
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.                        Tel: 314-747-6173
St. Louis, MO  63110                          Email: mha...@wustl.edu

From: <hcp-users-boun...@humanconnectome.org> on behalf of Scott Burwell 
Date: Friday, April 6, 2018 at 10:35 AM
To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed 
phase-encode file in "fmap" directory?

I want to use the HCP Pipeline BIDS app to preprocess T1w, T2w, and BOLD data 
collected at the CMRR. The BOLD data were acquired to apply the "PEpolar" 
method, whereby one short (TR=1.5s, 10 reps) set of EPI data were collected 
with AP phase-encoding, and one long (TR=1.5s, 400 reps) set of EPI data were 
collected with PA phase-encoding. Per BIDS specifications and others' 
suggestions (e.g., 
https://neurostars.org/t/fmriprep-docker-fieldmap-correction/623 ), I have 
stored the short acquisition AP data in the "fmap" directory and the long 
acquisition PA data in the "func" directory; the JSON sidecar for the "fmap" 
file points to the appropriate BOLD series via the "IntendedFor" key (see 
directory contents below).

I know that the HCP Pipeline BIDS app expects a fieldmap in order for the 
functional data to be preprocessed. However, based on documentation, I suspect 
the BIDS app in its current version does not support when the "fmap" is a 
paired reverse-phase encode image? I.e., the BIDS app does not sense that FSL's 
TOPUP should be used (rather than FUGUE or whatever program is currently used 
for this distortion correction). Has anyone else encountered this dilemma? Are 
there plans to add this functionality to the BIDS app?

Any information would be greatly appreciated. Thank you in advance.


##bids subject session directory contents:
cat ./fmap/sub-7536262_ses-00_acq-rest_dir-AP_run-01_epi.json
    "PhaseEncodingDirection": "j-",
    "IntendedFor": "func/sub-7536262_ses-00_task-rest_run-01_bold.nii.gz",
    "TotalReadoutTime": 0.0527996,

Scott J. Burwell, PhD
Postdoctoral Research Fellow
Department of Psychiatry
University of Minnesota, Minneapolis, MN

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