From 5b40ff12e229cc8cc15667c0bf049634c53c0448 Mon Sep 17 00:00:00 2001
From: sgiavasis <sgiava77@gmail.com>
Date: Tue, 29 May 2018 19:05:33 -0400
Subject: [PATCH] Included distortion correction pipeline config keys in the
 pipeline YAMLs.

---
 default_pipeline.yaml | 35 +++++++++++++++++++++++++++++++++++
 test_pipeline.yaml    | 40 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+)

diff --git a/default_pipeline.yaml b/default_pipeline.yaml
index 07e5978..f5e2e80 100644
--- a/default_pipeline.yaml
+++ b/default_pipeline.yaml
@@ -188,6 +188,41 @@ slice_timing_correction :  [1]
 slice_timing_pattern :  ['Use NIFTI Header']
 
 
+# Perform fieldmap correction using FSL FUGUE, with a single phase difference image, a subtraction of the two phase images from each echo.
+# Default scanner for this method is SIEMENS.
+runEPI_DistCorr :  [0]
+
+
+# Since the quality of the distortion heavily relies on the skull-stripping,
+# step, we provide a choice of method (AFNI 3dSkullStrip or FSL BET).
+# Options: ["BET", "3dSkullStrip"]
+fmap_distcorr_skullstrip: ["BET"]
+
+
+# Set the threshold value for the skull-stripping of the magnitude file.
+# Depending on the data, a tighter extraction may be necessary in order to
+# prevent noisy voxels from interfering with preparing the field map.
+# The default value is 0.5.
+fmap_distcorr_frac: [0.5]
+
+
+# Set the Delta-TE value, used for preparing the field map, the time delay between the first and second echo images.
+fmap_distcorr_deltaTE : 2.46
+
+
+# Set the Dwell time for FSL FUGUE. This is the time between scans.
+# The default value is commonly 0.00231s.
+fmap_distcorr_dwell_time : [0.0005]
+
+
+# Set the asymmetric ratio input value for FSL FUGUE.
+fmap_distcorr_dwell_asym_ratio : [0.93902439]
+
+
+# Set the phase-encoding direction. The options are: x, y, z, -x, -y, -z.
+fmap_distcorr_pedir: -y
+
+
 # Run Functional to Anatomical Registration
 runRegisterFuncToAnat :  [1]
 
diff --git a/test_pipeline.yaml b/test_pipeline.yaml
index 10753aa..a1cd164 100644
--- a/test_pipeline.yaml
+++ b/test_pipeline.yaml
@@ -192,18 +192,58 @@ stopIdx :  None
 # Default is None (TR information is read from image file header)
 TR :  None
 
+
 # Interpolate voxel time courses so they are sampled at the same time points.
 slice_timing_correction :  [1]
 
+
 # Acquisition strategy for acquiring image slices.
 slice_timing_pattern :  ['Use NIFTI Header']
 
+
+# Perform fieldmap correction using FSL FUGUE, with a single phase difference image, a subtraction of the two phase images from each echo.
+# Default scanner for this method is SIEMENS.
+runEPI_DistCorr :  [0]
+
+
+# Since the quality of the distortion heavily relies on the skull-stripping,
+# step, we provide a choice of method (AFNI 3dSkullStrip or FSL BET).
+# Options: ["BET", "3dSkullStrip"]
+fmap_distcorr_skullstrip: ["BET"]
+
+
+# Set the threshold value for the skull-stripping of the magnitude file.
+# Depending on the data, a tighter extraction may be necessary in order to
+# prevent noisy voxels from interfering with preparing the field map.
+# The default value is 0.5.
+fmap_distcorr_frac: [0.5]
+
+
+# Set the Delta-TE value, used for preparing the field map, the time delay between the first and second echo images.
+fmap_distcorr_deltaTE : 2.46
+
+
+# Set the Dwell time for FSL FUGUE. This is the time between scans.
+# The default value is commonly 0.00231s.
+fmap_distcorr_dwell_time : [0.0005]
+
+
+# Set the asymmetric ratio input value for FSL FUGUE.
+fmap_distcorr_dwell_asym_ratio : [0.93902439]
+
+
+# Set the phase-encoding direction. The options are: x, y, z, -x, -y, -z.
+fmap_distcorr_pedir: -y
+
+
 # Run Functional to Anatomical Registration
 runRegisterFuncToAnat :  [1]
 
+
 # Run Functional to Anatomical Registration with BB Register
 runBBReg :  [1]
 
+
 # Standard FSL 5.0 Scheduler used for Boundary Based Registration.
 # It is not necessary to change this path unless you intend to use non-standard MNI registration.
 boundaryBasedRegistrationSchedule :  /usr/share/fsl/5.0/etc/flirtsch/bbr.sch