From 6f52c0885ef12531e809c3eeafb703c13d8b562c Mon Sep 17 00:00:00 2001
From: dPys <dpisner@utexas.edu>
Date: Sun, 8 Sep 2019 00:00:48 -0500
Subject: [PATCH] reinvent dmriprep

correct hemi check

correct drop outliers

update cli
---
 dmriprep/.idea/dmriprep.iml                 |   13 +
 dmriprep/.idea/libraries/R_User_Library.xml |    6 +
 dmriprep/.idea/misc.xml                     |    7 +
 dmriprep/.idea/modules.xml                  |    8 +
 dmriprep/.idea/vcs.xml                      |    6 +
 dmriprep/.idea/workspace.xml                |  497 ++++++++
 dmriprep/__init__.py                        |    5 -
 dmriprep/b02b0.cnf                          |   26 +
 dmriprep/b02b0_1.cnf                        |   26 +
 dmriprep/cli.py                             |   55 +-
 dmriprep/core.py                            |  508 ++++++++
 dmriprep/data.py                            |   11 +-
 dmriprep/dmriprep.py                        |    6 -
 dmriprep/eddy_params.json                   |   19 +
 dmriprep/interfaces.py                      |  120 ++
 dmriprep/io.py                              |   59 +-
 dmriprep/qc.py                              |  411 ++++--
 dmriprep/run.py                             | 1249 ++++++-------------
 dmriprep/utils.py                           |   17 +-
 requirements.txt                            |   20 +-
 20 files changed, 2094 insertions(+), 975 deletions(-)
 create mode 100644 dmriprep/.idea/dmriprep.iml
 create mode 100644 dmriprep/.idea/libraries/R_User_Library.xml
 create mode 100644 dmriprep/.idea/misc.xml
 create mode 100644 dmriprep/.idea/modules.xml
 create mode 100644 dmriprep/.idea/vcs.xml
 create mode 100644 dmriprep/.idea/workspace.xml
 create mode 100644 dmriprep/b02b0.cnf
 create mode 100644 dmriprep/b02b0_1.cnf
 create mode 100644 dmriprep/core.py
 create mode 100644 dmriprep/eddy_params.json
 create mode 100644 dmriprep/interfaces.py

diff --git a/dmriprep/.idea/dmriprep.iml b/dmriprep/.idea/dmriprep.iml
new file mode 100644
index 0000000..86abb4c
--- /dev/null
+++ b/dmriprep/.idea/dmriprep.iml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.7 (PyNets)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="R Skeletons" level="application" />
+    <orderEntry type="library" name="R User Library" level="project" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/dmriprep/.idea/libraries/R_User_Library.xml b/dmriprep/.idea/libraries/R_User_Library.xml
new file mode 100644
index 0000000..71f5ff7
--- /dev/null
+++ b/dmriprep/.idea/libraries/R_User_Library.xml
@@ -0,0 +1,6 @@
+<component name="libraryTable">
+  <library name="R User Library">
+    <CLASSES />
+    <SOURCES />
+  </library>
+</component>
\ No newline at end of file
diff --git a/dmriprep/.idea/misc.xml b/dmriprep/.idea/misc.xml
new file mode 100644
index 0000000..1d8a5d6
--- /dev/null
+++ b/dmriprep/.idea/misc.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="JavaScriptSettings">
+    <option name="languageLevel" value="ES6" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.7 (PyNets)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/dmriprep/.idea/modules.xml b/dmriprep/.idea/modules.xml
new file mode 100644
index 0000000..3913f59
--- /dev/null
+++ b/dmriprep/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/dmriprep.iml" filepath="$PROJECT_DIR$/.idea/dmriprep.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/dmriprep/.idea/vcs.xml b/dmriprep/.idea/vcs.xml
new file mode 100644
index 0000000..6c0b863
--- /dev/null
+++ b/dmriprep/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/dmriprep/.idea/workspace.xml b/dmriprep/.idea/workspace.xml
new file mode 100644
index 0000000..733e5cb
--- /dev/null
+++ b/dmriprep/.idea/workspace.xml
@@ -0,0 +1,497 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="8c1c3603-9fb8-4739-a815-d51b6f24a6f7" name="Default Changelist" comment="">
+<<<<<<< HEAD
+      <change beforePath="$PROJECT_DIR$/core.py" beforeDir="false" afterPath="$PROJECT_DIR$/core.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/run.py" beforeDir="false" afterPath="$PROJECT_DIR$/run.py" afterDir="false" />
+=======
+      <change beforePath="$PROJECT_DIR$/io.py" beforeDir="false" afterPath="$PROJECT_DIR$/io.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/qc.py" beforeDir="false" afterPath="$PROJECT_DIR$/qc.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/run.py" beforeDir="false" afterPath="$PROJECT_DIR$/run.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/utils.py" beforeDir="false" afterPath="$PROJECT_DIR$/utils.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/../requirements.txt" beforeDir="false" afterPath="$PROJECT_DIR$/../requirements.txt" afterDir="false" />
+>>>>>>> reinvent dmriprep
+    </list>
+    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="FileEditorManager">
+<<<<<<< HEAD
+    <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/run.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="497">
+              <caret line="339" column="7" selection-start-line="339" selection-start-column="7" selection-end-line="339" selection-end-column="7" />
+=======
+    <leaf>
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/run.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="255">
+              <caret line="17" column="33" lean-forward="true" selection-start-line="17" selection-start-column="33" selection-end-line="17" selection-end-column="33" />
+>>>>>>> reinvent dmriprep
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/utils.py">
+          <provider selected="true" editor-type-id="text-editor">
+<<<<<<< HEAD
+            <state relative-caret-position="351">
+              <caret line="50" column="23" selection-start-line="50" selection-start-column="23" selection-end-line="50" selection-end-column="23" />
+              <folding>
+                <element signature="e#48#66#0" expanded="true" />
+=======
+            <state relative-caret-position="135">
+              <caret line="9" column="40" lean-forward="true" selection-start-line="9" selection-start-column="40" selection-end-line="9" selection-end-column="40" />
+              <folding>
+                <element signature="e#48#64#0" expanded="true" />
+>>>>>>> reinvent dmriprep
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/qc.py">
+          <provider selected="true" editor-type-id="text-editor">
+<<<<<<< HEAD
+            <state relative-caret-position="-2312">
+              <caret line="27" column="34" lean-forward="true" selection-start-line="27" selection-start-column="34" selection-end-line="27" selection-end-column="34" />
+=======
+            <state relative-caret-position="270">
+              <caret line="18" column="28" selection-start-line="18" selection-start-column="28" selection-end-line="18" selection-end-column="28" />
+>>>>>>> reinvent dmriprep
+              <folding>
+                <element signature="e#0#13#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/core.py">
+          <provider selected="true" editor-type-id="text-editor">
+<<<<<<< HEAD
+            <state relative-caret-position="1926">
+              <caret line="322" column="63" lean-forward="true" selection-start-line="322" selection-start-column="63" selection-end-line="322" selection-end-column="63" />
+=======
+            <state relative-caret-position="630">
+              <caret line="42" column="14" lean-forward="true" selection-start-line="42" selection-start-column="14" selection-end-line="42" selection-end-column="14" />
+>>>>>>> reinvent dmriprep
+              <folding>
+                <element signature="e#0#9#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+<<<<<<< HEAD
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/dmriprep.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="105">
+              <caret line="7" selection-start-line="7" selection-end-line="7" />
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/interfaces.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="840">
+              <caret line="56" column="55" selection-start-line="56" selection-start-column="55" selection-end-line="56" selection-end-column="55" />
+              <folding>
+                <element signature="e#0#9#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+      <file pinned="false" current-in-tab="false">
+        <entry file="file://$PROJECT_DIR$/io.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="370">
+              <caret line="92" column="34" lean-forward="true" selection-start-line="92" selection-start-column="34" selection-end-line="92" selection-end-column="34" />
+              <folding>
+                <element signature="e#67#76#0" expanded="true" />
+              </folding>
+            </state>
+          </provider>
+        </entry>
+      </file>
+=======
+>>>>>>> reinvent dmriprep
+    </leaf>
+  </component>
+  <component name="FindInProjectRecents">
+    <findStrings>
+      <find>aparc</find>
+      <find>get_eddy_args_node</find>
+      <find>_inputs_node</find>
+      <find>check_shelled</find>
+      <find>save_json</find>
+      <find>load_json</find>
+      <find>make_mean_b0</find>
+      <find>make_mean_b0_node</find>
+      <find>'mean_file_out'</find>
+      <find>btr</find>
+      <find>mean</find>
+      <find>make_gtab_and_b0s_node</find>
+      <find>topup_inputs_from_dwi_files</find>
+      <find>slicetime_lookup</find>
+      <find>get_topup_inputs_node</find>
+      <find>img</find>
+      <find>denoise_node</find>
+      <find>apply_mask_premoco_node</find>
+      <find>btr_node</find>
+      <find>make_gtab_and_b0s</find>
+      <find>itertools</find>
+<<<<<<< HEAD
+      <find>get_eddy_inputs_node</find>
+      <find>get_eddy_inputs</find>
+      <find>eddy</find>
+      <find>eddy_inputs_from_dwi_files</find>
+      <find>make_gtab_node</find>
+      <find>eddy_node</find>
+      <find>bvecs_reor</find>
+      <find>drop_outliers_fn_node</find>
+=======
+>>>>>>> reinvent dmriprep
+    </findStrings>
+    <replaceStrings>
+      <replace>correct_vecs_and_make_b0s</replace>
+    </replaceStrings>
+  </component>
+  <component name="Git.Settings">
+    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$/.." />
+  </component>
+  <component name="IdeDocumentHistory">
+    <option name="CHANGED_PATHS">
+      <list>
+        <option value="$PROJECT_DIR$/io.py" />
+<<<<<<< HEAD
+        <option value="$PROJECT_DIR$/qc.py" />
+        <option value="$PROJECT_DIR$/utils.py" />
+        <option value="$PROJECT_DIR$/interfaces.py" />
+        <option value="$PROJECT_DIR$/run.py" />
+=======
+        <option value="$PROJECT_DIR$/interfaces.py" />
+        <option value="$PROJECT_DIR$/qc.py" />
+        <option value="$PROJECT_DIR$/run.py" />
+        <option value="$PROJECT_DIR$/utils.py" />
+>>>>>>> reinvent dmriprep
+        <option value="$PROJECT_DIR$/core.py" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectConfigurationFiles">
+    <option name="files">
+      <list>
+        <option value="$PROJECT_DIR$/.idea/dmriprep.iml" />
+        <option value="$PROJECT_DIR$/.idea/misc.xml" />
+        <option value="$PROJECT_DIR$/.idea/modules.xml" />
+        <option value="$PROJECT_DIR$/.idea/vcs.xml" />
+        <option value="$PROJECT_DIR$/.idea/libraries/R_User_Library.xml" />
+        <option value="$PROJECT_DIR$/.idea/dmriprep.iml" />
+        <option value="$PROJECT_DIR$/.idea/misc.xml" />
+        <option value="$PROJECT_DIR$/.idea/vcs.xml" />
+        <option value="$PROJECT_DIR$/.idea/modules.xml" />
+        <option value="$PROJECT_DIR$/.idea/libraries/R_User_Library.xml" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectFrameBounds">
+<<<<<<< HEAD
+    <option name="x" value="404" />
+    <option name="y" value="23" />
+=======
+    <option name="x" value="350" />
+    <option name="y" value="24" />
+>>>>>>> reinvent dmriprep
+    <option name="width" value="1276" />
+    <option name="height" value="985" />
+  </component>
+  <component name="ProjectLevelVcsManager" settingsEditedManually="true" />
+  <component name="ProjectView">
+    <navigator proportions="" version="1">
+      <foldersAlwaysOnTop value="true" />
+    </navigator>
+    <panes>
+<<<<<<< HEAD
+      <pane id="Scope" />
+=======
+>>>>>>> reinvent dmriprep
+      <pane id="ProjectPane">
+        <subPane>
+          <expand>
+            <path>
+              <item name="dmriprep" type="b2602c69:ProjectViewProjectNode" />
+              <item name="dmriprep" type="462c0819:PsiDirectoryNode" />
+            </path>
+            <path>
+              <item name="dmriprep" type="b2602c69:ProjectViewProjectNode" />
+              <item name="Scratches and Consoles" type="1a2a3e82:ScratchProjectViewPane$MyProjectNode" />
+            </path>
+          </expand>
+          <select />
+        </subPane>
+      </pane>
+<<<<<<< HEAD
+=======
+      <pane id="Scope" />
+>>>>>>> reinvent dmriprep
+    </panes>
+  </component>
+  <component name="PropertiesComponent">
+    <property name="ASKED_SHARE_PROJECT_CONFIGURATION_FILES" value="true" />
+<<<<<<< HEAD
+    <property name="SHARE_PROJECT_CONFIGURATION_FILES" value="true" />
+=======
+>>>>>>> reinvent dmriprep
+    <property name="WebServerToolWindowFactoryState" value="false" />
+    <property name="last_opened_file_path" value="$PROJECT_DIR$" />
+    <property name="nodejs_interpreter_path.stuck_in_default_project" value="undefined stuck path" />
+    <property name="nodejs_npm_path_reset_for_default_project" value="true" />
+<<<<<<< HEAD
+    <property name="run.code.analysis.last.selected.profile" value="pProject Default" />
+    <property name="settings.editor.selected.configurable" value="preferences.externalTools" />
+=======
+    <property name="settings.editor.selected.configurable" value="com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable" />
+>>>>>>> reinvent dmriprep
+  </component>
+  <component name="RunDashboard">
+    <option name="ruleStates">
+      <list>
+        <RuleState>
+          <option name="name" value="ConfigurationTypeDashboardGroupingRule" />
+        </RuleState>
+        <RuleState>
+          <option name="name" value="StatusDashboardGroupingRule" />
+        </RuleState>
+      </list>
+    </option>
+  </component>
+  <component name="SvnConfiguration">
+    <configuration />
+  </component>
+  <component name="TaskManager">
+    <task active="true" id="Default" summary="Default task">
+      <changelist id="8c1c3603-9fb8-4739-a815-d51b6f24a6f7" name="Default Changelist" comment="" />
+      <created>1566137307717</created>
+      <option name="number" value="Default" />
+      <option name="presentableId" value="Default" />
+      <updated>1566137307717</updated>
+      <workItem from="1566137311298" duration="539000" />
+      <workItem from="1567887418786" duration="2978000" />
+<<<<<<< HEAD
+      <workItem from="1567890546884" duration="15654000" />
+      <workItem from="1567921545309" duration="2847000" />
+=======
+      <workItem from="1567890546884" duration="13911000" />
+>>>>>>> reinvent dmriprep
+    </task>
+    <servers />
+  </component>
+  <component name="TimeTrackingManager">
+<<<<<<< HEAD
+    <option name="totallyTimeSpent" value="22018000" />
+  </component>
+  <component name="ToolWindowManager">
+    <frame x="404" y="23" width="1276" height="985" extended-state="0" />
+    <editor active="true" />
+    <layout>
+      <window_info active="true" content_ui="combo" id="Project" order="0" visible="true" weight="0.09724473" />
+=======
+    <option name="totallyTimeSpent" value="17428000" />
+  </component>
+  <component name="ToolWindowManager">
+    <frame x="350" y="24" width="1276" height="985" extended-state="0" />
+    <editor active="true" />
+    <layout>
+      <window_info active="true" content_ui="combo" id="Project" order="0" visible="true" weight="0.095623985" />
+>>>>>>> reinvent dmriprep
+      <window_info id="Structure" order="1" side_tool="true" weight="0.25" />
+      <window_info id="aws.explorer" order="2" side_tool="true" />
+      <window_info id="Favorites" order="3" side_tool="true" />
+      <window_info anchor="bottom" id="Message" order="0" />
+      <window_info anchor="bottom" id="Find" order="1" />
+<<<<<<< HEAD
+      <window_info active="true" anchor="bottom" id="Run" order="2" visible="true" weight="0.32922733" />
+=======
+      <window_info anchor="bottom" id="Run" order="2" />
+>>>>>>> reinvent dmriprep
+      <window_info anchor="bottom" id="Debug" order="3" weight="0.4" />
+      <window_info anchor="bottom" id="Cvs" order="4" weight="0.25" />
+      <window_info anchor="bottom" id="Inspection" order="5" weight="0.4" />
+      <window_info anchor="bottom" id="TODO" order="6" />
+      <window_info anchor="bottom" id="Docker" order="7" />
+      <window_info anchor="bottom" id="Version Control" order="8" />
+      <window_info anchor="bottom" id="Database Changes" order="9" />
+      <window_info anchor="bottom" id="Event Log" order="10" side_tool="true" />
+<<<<<<< HEAD
+      <window_info anchor="bottom" id="Terminal" order="11" weight="0.32922733" />
+=======
+      <window_info anchor="bottom" id="Terminal" order="11" />
+>>>>>>> reinvent dmriprep
+      <window_info anchor="bottom" id="Python Console" order="12" weight="0.32922733" />
+      <window_info anchor="right" id="Commander" internal_type="SLIDING" order="0" type="SLIDING" weight="0.4" />
+      <window_info anchor="right" id="Ant Build" order="1" weight="0.25" />
+      <window_info anchor="right" content_ui="combo" id="Hierarchy" order="2" weight="0.25" />
+      <window_info anchor="right" id="SciView" order="3" />
+      <window_info anchor="right" id="R Graphics" order="4" />
+      <window_info anchor="right" id="R Packages" order="5" />
+      <window_info anchor="right" id="Database" order="6" />
+    </layout>
+  </component>
+  <component name="TypeScriptGeneratedFilesManager">
+    <option name="version" value="1" />
+  </component>
+  <component name="editorHistoryManager">
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/data.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state>
+          <folding>
+            <element signature="e#70#81#0" expanded="true" />
+=======
+    <entry file="file://$PROJECT_DIR$/dmriprep.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="120">
+          <caret line="8" lean-forward="true" selection-start-line="8" selection-end-line="8" />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/interfaces.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="795">
+          <caret line="53" column="53" selection-start-line="53" selection-start-column="53" selection-end-line="53" selection-end-column="53" />
+          <folding>
+            <element signature="e#0#9#0" expanded="true" />
+>>>>>>> reinvent dmriprep
+          </folding>
+        </state>
+      </provider>
+    </entry>
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/b02b0_1.cnf">
+      <provider selected="true" editor-type-id="text-editor" />
+    </entry>
+    <entry file="file://$PROJECT_DIR$/io.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="370">
+          <caret line="92" column="34" lean-forward="true" selection-start-line="92" selection-start-column="34" selection-end-line="92" selection-end-column="34" />
+=======
+    <entry file="file://$PROJECT_DIR$/io.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="1275">
+          <caret line="85" lean-forward="true" selection-start-line="85" selection-end-line="85" />
+>>>>>>> reinvent dmriprep
+          <folding>
+            <element signature="e#67#76#0" expanded="true" />
+          </folding>
+        </state>
+      </provider>
+    </entry>
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/interfaces.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="840">
+          <caret line="56" column="55" selection-start-line="56" selection-start-column="55" selection-end-line="56" selection-end-column="55" />
+          <folding>
+            <element signature="e#0#9#0" expanded="true" />
+=======
+    <entry file="file://$PROJECT_DIR$/data.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state>
+          <folding>
+            <element signature="e#70#81#0" expanded="true" />
+>>>>>>> reinvent dmriprep
+          </folding>
+        </state>
+      </provider>
+    </entry>
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/dmriprep.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="105">
+          <caret line="7" selection-start-line="7" selection-end-line="7" />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/qc.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="-2312">
+          <caret line="27" column="34" lean-forward="true" selection-start-line="27" selection-start-column="34" selection-end-line="27" selection-end-column="34" />
+          <folding>
+            <element signature="e#0#13#0" expanded="true" />
+=======
+    <entry file="file://$PROJECT_DIR$/run.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="255">
+          <caret line="17" column="33" lean-forward="true" selection-start-line="17" selection-start-column="33" selection-end-line="17" selection-end-column="33" />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/utils.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="135">
+          <caret line="9" column="40" lean-forward="true" selection-start-line="9" selection-start-column="40" selection-end-line="9" selection-end-column="40" />
+          <folding>
+            <element signature="e#48#64#0" expanded="true" />
+>>>>>>> reinvent dmriprep
+          </folding>
+        </state>
+      </provider>
+    </entry>
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/utils.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="351">
+          <caret line="50" column="23" selection-start-line="50" selection-start-column="23" selection-end-line="50" selection-end-column="23" />
+          <folding>
+            <element signature="e#48#66#0" expanded="true" />
+=======
+    <entry file="file://$PROJECT_DIR$/qc.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="270">
+          <caret line="18" column="28" selection-start-line="18" selection-start-column="28" selection-end-line="18" selection-end-column="28" />
+          <folding>
+            <element signature="e#0#13#0" expanded="true" />
+>>>>>>> reinvent dmriprep
+          </folding>
+        </state>
+      </provider>
+    </entry>
+<<<<<<< HEAD
+    <entry file="file://$PROJECT_DIR$/run.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="497">
+          <caret line="339" column="7" selection-start-line="339" selection-start-column="7" selection-end-line="339" selection-end-column="7" />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/core.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="1926">
+          <caret line="322" column="63" lean-forward="true" selection-start-line="322" selection-start-column="63" selection-end-line="322" selection-end-column="63" />
+=======
+    <entry file="file://$PROJECT_DIR$/core.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="630">
+          <caret line="42" column="14" lean-forward="true" selection-start-line="42" selection-start-column="14" selection-end-line="42" selection-end-column="14" />
+>>>>>>> reinvent dmriprep
+          <folding>
+            <element signature="e#0#9#0" expanded="true" />
+          </folding>
+        </state>
+      </provider>
+    </entry>
+  </component>
+</project>
\ No newline at end of file
diff --git a/dmriprep/__init__.py b/dmriprep/__init__.py
index 6150760..fa3abe6 100644
--- a/dmriprep/__init__.py
+++ b/dmriprep/__init__.py
@@ -16,11 +16,6 @@
 warnings.filterwarnings("ignore", message="numpy.dtype size changed")
 warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
 
-from . import data
-from . import io
-from . import qc
-from . import run
-
 module_logger = logging.getLogger(__name__)
 
 # get the log level from environment variable
diff --git a/dmriprep/b02b0.cnf b/dmriprep/b02b0.cnf
new file mode 100644
index 0000000..77c4cd5
--- /dev/null
+++ b/dmriprep/b02b0.cnf
@@ -0,0 +1,26 @@
+# Resolution (knot-spacing) of warps in mm
+--warpres=20,16,14,12,10,6,4,4,4
+# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel)
+--subsamp=2,2,2,2,2,1,1,1,1
+# FWHM of gaussian smoothing
+--fwhm=8,6,4,3,3,2,1,0,0
+# Maximum number of iterations
+--miter=5,5,5,5,5,10,10,20,20
+# Relative weight of regularisation
+--lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001
+# If set to 1 lambda is multiplied by the current average squared difference
+--ssqlambda=1
+# Regularisation model
+--regmod=bending_energy
+# If set to 1 movements are estimated along with the field
+--estmov=1,1,1,1,1,0,0,0,0
+# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient
+--minmet=0,0,0,0,0,1,1,1,1
+# Quadratic or cubic splines
+--splineorder=3
+# Precision for calculation and storage of Hessian
+--numprec=double
+# Linear or spline interpolation
+--interp=spline
+# If set to 1 the images are individually scaled to a common mean intensity 
+--scale=1
\ No newline at end of file
diff --git a/dmriprep/b02b0_1.cnf b/dmriprep/b02b0_1.cnf
new file mode 100644
index 0000000..a15519e
--- /dev/null
+++ b/dmriprep/b02b0_1.cnf
@@ -0,0 +1,26 @@
+# Resolution (knot-spacing) of warps in mm
+--warpres=20,16,14,12,10,6,4,4,4
+# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel)
+--subsamp=1,1,1,1,1,1,1,1,1
+# FWHM of gaussian smoothing
+--fwhm=8,6,4,3,3,2,1,0,0
+# Maximum number of iterations
+--miter=5,5,5,5,5,10,10,20,20
+# Relative weight of regularisation
+--lambda=0.0005,0.0001,0.00001,0.0000015,0.0000005,0.0000005,0.00000005,0.0000000005,0.00000000001
+# If set to 1 lambda is multiplied by the current average squared difference
+--ssqlambda=1
+# Regularisation model
+--regmod=bending_energy
+# If set to 1 movements are estimated along with the field
+--estmov=1,1,1,1,1,0,0,0,0
+# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient
+--minmet=0,0,0,0,0,1,1,1,1
+# Quadratic or cubic splines
+--splineorder=3
+# Precision for calculation and storage of Hessian
+--numprec=double
+# Linear or spline interpolation
+--interp=spline
+# If set to 1 the images are individually scaled to a common mean intensity 
+--scale=1
\ No newline at end of file
diff --git a/dmriprep/cli.py b/dmriprep/cli.py
index 8b45d7e..48a4f98 100644
--- a/dmriprep/cli.py
+++ b/dmriprep/cli.py
@@ -18,7 +18,7 @@
 
 
 @click.command()
-@click.option('--participant-label',
+@click.option('--participant_label',
               help="The label(s) of the participant(s) that should be"
                    "analyzed. The label corresponds to"
                    "sub-<participant_label> from the BIDS spec (so it does"
@@ -26,29 +26,38 @@
                    "all subjects will be analyzed. Multiple participants"
                    "can be specified with a space separated list.",
               default=None)
-@click.option('--eddy-niter',
-              help="Fixed number of eddy iterations. See "
-                   "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide"
-                   "#A--niter",
-              default=5, type=(int))
-@click.option('--slice-outlier-threshold',
+@click.option('--session',
+              help="The session number off the participant data in the case of multiple sessions.",
+              default=1)
+@click.option('--denoise_strategy',
+              help="Denoising strategy. Options are: mppca, localpca, or nlmeans.",
+              default="mppca")
+@click.option('--slice_outlier_threshold',
               help="Number of allowed outlier slices per volume. "
                    "If this is exceeded the volume is dropped from analysis. "
                    "If an int is provided, it is treated as number of allowed "
                    "outlier slices. If a float between 0 and 1 "
                    "(exclusive) is provided, it is treated the fraction of "
                    "allowed outlier slices.",
-              default=0.02)
+              default=0.05)
 @click.argument('bids_dir',
                 )
 @click.argument('output_dir',
                 )
+@click.option('--plugin',
+              help="Scheduling plugin type. Default is MultiProc.",
+              default="MultiProc")
+@click.option('--vox',
+              help="Voxel resolution. Default is 2mm.",
+              default='2mm')
+@click.option('--verbose',
+              help="Verbose logging. Default is False.",
+              default=False)
 @click.argument('analysis_level',
                 type=click.Choice(['participant', 'group']),
                 default='participant')
-def main(participant_label, bids_dir, output_dir,
-         eddy_niter=5, slice_outlier_threshold=0.02,
-         analysis_level="participant"):
+def main(participant_label, session, bids_dir, output_dir, plugin_type='MultiProc', verbose=False,
+         denoise_strategy="mppca", slice_outlier_threshold=0.05, vox_size='2mm', analysis_level="participant"):
     """
     BIDS_DIR: The directory with the input dataset formatted according to
     the BIDS standard.
@@ -66,20 +75,24 @@ def main(participant_label, bids_dir, output_dir,
         raise NotImplementedError('The only valid analysis level for dmriprep '
                                   'is participant at the moment.')
 
-    inputs = io.get_bids_files(participant_label, bids_dir)
+    from dmriprep.io import get_bids_layout
 
-    for subject_inputs in inputs:
-        run.run_dmriprep_pe(**subject_inputs,
-                            working_dir=os.path.join(output_dir, 'scratch'),
-                            out_dir=output_dir,
-                            eddy_niter=eddy_niter,
-                            slice_outlier_threshold=slice_outlier_threshold)
+    sub_dict = get_bids_layout(bids_dir, participant_label, session)
+    dwi = sub_dict[session]['dwi']
+    fbvec = sub_dict[session]['bvec']
+    fbval = sub_dict[session]['bval']
+    metadata = sub_dict[session]['metadata']
+
+    wf = run.init_single_subject_wf(dwi, fbvec, fbval, metadata, out_dir=output_dir, strategy=denoise_strategy,
+                                    vox_size=vox_size, plugin_type=plugin_type, outlier_thresh=slice_outlier_threshold,
+                                    verbose=verbose)
+    wf.run()
 
     return 0
 
+
 @click.command()
-@click.argument('output_dir',
-                )
+@click.argument('output_dir')
 @click.option('--subject', help="subject id to download (will choose 1 subject if not specified",
               default="sub-NDARBA507GCT")
 @click.option('--study', help="which study to download. Right now we only support the HBN dataset",
@@ -126,7 +139,7 @@ def upload(output_dir, bucket, access_key, secret_key, provider='s3', subject=No
         output_dir += '/'
 
     if provider == 's3' or provider == 'S3':
-        client = boto3.client('s3',  aws_access_key_id=access_key, aws_secret_access_key=secret_key)
+        client = boto3.client('s3', aws_access_key_id=access_key, aws_secret_access_key=secret_key)
 
         if subject is not None:
             assert os.path.exists(os.path.join(output_dir, subject)), 'this subject id does not exist!'
diff --git a/dmriprep/core.py b/dmriprep/core.py
new file mode 100644
index 0000000..2a297fb
--- /dev/null
+++ b/dmriprep/core.py
@@ -0,0 +1,508 @@
+import os
+
+import nibabel as nib
+import numpy as np
+
+
+def make_gtab(fbval, fbvec, sesdir):
+    from dipy.io import save_pickle
+    from dipy.core.gradients import gradient_table
+    from dipy.io import read_bvals_bvecs
+
+    if fbval and fbvec:
+        bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
+    else:
+        raise ValueError("Either bvals or bvecs files not found (or rescaling failed)!")
+
+    namer_dir = sesdir + "/dmri_tmp"
+    if not os.path.isdir(namer_dir):
+        os.mkdir(namer_dir)
+
+    gtab_file = "%s%s" % (namer_dir, "/gtab.pkl")
+
+    # Creating the gradient table
+    gtab = gradient_table(bvals, bvecs)
+
+    # Correct b0 threshold
+    gtab.b0_threshold = min(bvals)
+
+    # Show info
+    print(gtab.info)
+
+    # Save gradient table to pickle
+    save_pickle(gtab_file, gtab)
+
+    return gtab_file, gtab
+
+
+def rescale_bvec(bvec, bvec_rescaled):
+    """
+    Normalizes b-vectors to be of unit length for the non-zero b-values. If the
+    b-value is 0, the vector is untouched.
+
+    Parameters
+    ----------
+    bvec : str
+        File name of the original b-vectors file.
+    bvec_rescaled : str
+        File name of the new (normalized) b-vectors file. Must have extension `.bvec`.
+
+    Returns
+    -------
+    bvec_rescaled : str
+        File name of the new (normalized) b-vectors file. Must have extension `.bvec`.
+    """
+    bv1 = np.array(np.loadtxt(bvec))
+    # Enforce proper dimensions
+    bv1 = bv1.T if bv1.shape[0] == 3 else bv1
+
+    # Normalize values not close to norm 1
+    bv2 = [
+        b / np.linalg.norm(b) if not np.isclose(np.linalg.norm(b), 0) else b
+        for b in bv1
+    ]
+    np.savetxt(bvec_rescaled, bv2)
+    return bvec_rescaled
+
+
+def correct_vecs_and_make_b0s(fbval, fbvec, dwi_file, sesdir):
+    from dipy.io import read_bvals_bvecs
+    from dmriprep.core import make_gtab, rescale_bvec
+    from dmriprep.utils import is_hemispherical
+
+    namer_dir = sesdir + "/dmri_tmp"
+    if not os.path.isdir(namer_dir):
+        os.mkdir(namer_dir)
+
+    bvec_rescaled = "%s%s" % (namer_dir, "/bvec_scaled.bvec")
+
+    # loading bvecs/bvals
+    bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
+    bvecs[np.where(np.any(abs(bvecs) >= 10, axis=1) == True)] = [1, 0, 0]
+    bvecs[np.where(bvals == 0)] = 0
+    if (
+        len(
+            bvecs[
+                np.where(
+                    np.logical_and(
+                        bvals > 50, np.all(abs(bvecs) == np.array([0, 0, 0]), axis=1)
+                    )
+                )
+            ]
+        )
+        > 0
+    ):
+        raise ValueError(
+            "WARNING: Encountered potentially corrupted bval/bvecs. Check to ensure volumes with a "
+            "diffusion weighting are not being treated as B0's along the bvecs"
+        )
+    np.savetxt(fbval, bvals)
+    np.savetxt(fbvec, bvecs)
+    bvec_rescaled = rescale_bvec(fbvec, bvec_rescaled)
+    vecs_rescaled = np.genfromtxt(bvec_rescaled)
+    vecs = np.round(vecs_rescaled, 8)[~(np.round(vecs_rescaled, 8) == 0).all(1)]
+    [is_hemi, pole] = is_hemispherical(vecs)
+    if is_hemi is True:
+        raise ValueError(
+            "B-vectors for this data are hemispherical and therefore use of topup/eddy routines is not "
+            "advised"
+        )
+
+    [gtab_file, gtab] = make_gtab(fbval, bvec_rescaled, sesdir)
+
+    # Get b0 indices
+    b0s = np.where(gtab.bvals == gtab.b0_threshold)[0].tolist()
+    print("%s%s" % ("b0's found at: ", b0s))
+    firstb0 = b0s[0]
+
+    # Extract and Combine all b0s collected
+    print("Extracting b0's...")
+    b0_vols = []
+    dwi_img = nib.load(dwi_file)
+    dwi_data = dwi_img.get_data()
+    for b0 in b0s:
+        print(b0)
+        b0_vols.append(dwi_data[:, :, :, b0])
+
+    firstb0_file = sesdir + "/firstb0.nii.gz"
+    nib.save(
+        nib.Nifti1Image(
+            b0_vols[firstb0].astype(np.float32), dwi_img.affine, dwi_img.header
+        ),
+        firstb0_file,
+    )
+
+    return firstb0, firstb0_file, gtab_file, b0_vols, b0s
+
+
+def topup_inputs_from_dwi_files(dwi, sesdir, spec_acqp, b0_vols, topup_config_odd):
+    from collections import defaultdict
+
+    """Create a datain spec and a slspec from a list of dwi files."""
+    # Write the datain.txt file
+    datain_lines = []
+    spec_counts = defaultdict(int)
+
+    dwi_img = nib.load(dwi)
+    imain_data = []
+    for b0_vol in b0_vols:
+        num_trs = 1 if len(b0_vol.shape) < 4 else b0_vol.shape[3]
+        datain_lines.extend([spec_acqp] * num_trs)
+        spec_counts[spec_acqp] += num_trs
+        imain_data.append(b0_vol)
+
+    # Make a 4d series
+    imain_output = sesdir + "/topup_imain.nii.gz"
+    imain_data_4d = [imain_vol[..., np.newaxis] for imain_vol in imain_data]
+    imain_img = nib.Nifti1Image(
+        np.concatenate(imain_data_4d, 3), dwi_img.affine, dwi_img.header
+    )
+    assert imain_img.shape[3] == len(datain_lines)
+    imain_img.to_filename(imain_output)
+
+    # Write the datain text file
+    datain_file = sesdir + "/acqparams.txt"
+    with open(datain_file, "w") as f:
+        f.write("\n".join(datain_lines))
+
+    example_b0 = b0_vols[0]
+    topup_config = "b02b0.cnf"
+    if 1 in (example_b0.shape[0] % 2, example_b0.shape[1] % 2, example_b0.shape[2] % 2):
+        print("Using slower b02b0_1.cnf because an axis has an odd number of slices")
+        topup_config = topup_config_odd
+
+    return datain_file, imain_output, example_b0, datain_lines, topup_config
+
+
+def eddy_inputs_from_dwi_files(sesdir, gtab_file):
+    from dipy.io import load_pickle
+
+    b0s_mask_all = []
+    gtab = load_pickle(gtab_file)
+    b0s_mask = gtab.b0s_mask
+    b0s_mask_all.append(b0s_mask)
+
+    # Create the index file
+    index_file = sesdir + "/index.txt"
+    ix_vec = []
+    i = 1
+    pastfirst0s = False
+    for val in gtab.bvals:
+        if val > gtab.b0_threshold:
+            pastfirst0s = True
+        elif val <= gtab.b0_threshold and pastfirst0s is True:
+            i = i + 1
+        ix_vec.append(i)
+    with open(index_file, "w") as f:
+        f.write(" ".join(map(str, ix_vec)))
+
+    return index_file
+
+
+def id_outliers_fn(outlier_report, threshold, dwi_file):
+    """Get list of scans that exceed threshold for number of outliers
+    Parameters
+    ----------
+    outlier_report: string
+        Path to the fsl_eddy outlier report
+    threshold: int or float
+        If threshold is an int, it is treated as number of allowed outlier
+        slices. If threshold is a float between 0 and 1 (exclusive), it is
+        treated the fraction of allowed outlier slices before we drop the
+        whole volume.
+    dwi_file: string
+        Path to nii dwi file to determine total number of slices
+    Returns
+    -------
+    drop_scans: numpy.ndarray
+        List of scan indices to drop
+    """
+    import nibabel as nib
+    import numpy as np
+    import os.path as op
+    import parse
+
+    with open(op.abspath(outlier_report), "r") as fp:
+        lines = fp.readlines()
+
+    p = parse.compile(
+        "Slice {slice:d} in scan {scan:d} is an outlier with "
+        "mean {mean_sd:f} standard deviations off, and mean "
+        "squared {mean_sq_sd:f} standard deviations off."
+    )
+
+    outliers = [p.parse(l).named for l in lines]
+    scans = {d["scan"] for d in outliers}
+
+    def num_outliers(scan, outliers):
+        return len([d for d in outliers if d["scan"] == scan])
+
+    if 0 < threshold < 1:
+        img = nib.load(dwi_file)
+        try:
+            threshold *= img.header.get_n_slices()
+        except nib.spatialimages.HeaderDataError:
+            print(
+                "WARNING. We are not sure which dimension has the "
+                "slices in this image. So we are using the 3rd dim.",
+                img.shape,
+            )
+            threshold *= img.shape[2]
+
+    drop_scans = np.array([s for s in scans if num_outliers(s, outliers) > threshold])
+
+    outpath = op.abspath("dropped_scans.txt")
+    np.savetxt(outpath, drop_scans, fmt="%d")
+
+    return drop_scans, outpath
+
+
+def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
+    """Drop outlier volumes from dwi file
+    Parameters
+    ----------
+    in_file: string
+        Path to nii dwi file to drop outlier volumes from
+    in_bval: string
+        Path to bval file to drop outlier volumes from
+    in_bvec: string
+        Path to bvec file to drop outlier volumes from
+    drop_scans: numpy.ndarray or str
+        List of scan indices to drop. If str, then assume path to text file
+        listing outlier volumes.
+
+    Returns
+    -------
+    out_file: string
+        Path to "thinned" output dwi file
+    out_bval: string
+        Path to "thinned" output bval file
+    out_bvec: string
+        Path to "thinned" output bvec file
+    """
+    import nibabel as nib
+    import numpy as np
+    import os.path as op
+    from nipype.utils.filemanip import fname_presuffix
+
+    if isinstance(drop_scans, str):
+        try:
+            drop_scans = np.genfromtxt(drop_scans)
+        except TypeError:
+            print(
+                "Unrecognized file format. Unable to load vector from drop_scans file."
+            )
+
+    img = nib.load(op.abspath(in_file))
+    img_data = img.get_data()
+    img_data_thinned = np.delete(img_data, drop_scans, axis=3)
+    if isinstance(img, nib.nifti1.Nifti1Image):
+        img_thinned = nib.Nifti1Image(
+            img_data_thinned.astype(np.float64), img.affine, header=img.header
+        )
+    elif isinstance(img, nib.nifti2.Nifti2Image):
+        img_thinned = nib.Nifti2Image(
+            img_data_thinned.astype(np.float64), img.affine, header=img.header
+        )
+    else:
+        raise TypeError("in_file does not contain Nifti image datatype.")
+
+    out_file = fname_presuffix(in_file, suffix="_thinned", newpath=op.abspath("."))
+    nib.save(img_thinned, op.abspath(out_file))
+
+    bval = np.loadtxt(in_bval)
+    bval_thinned = np.delete(bval, drop_scans, axis=0)
+    out_bval = fname_presuffix(in_bval, suffix="_thinned", newpath=op.abspath("."))
+    np.savetxt(out_bval, bval_thinned)
+
+    bvec = np.loadtxt(in_bvec)
+    bvec_thinned = np.delete(bvec, drop_scans, axis=0)
+    out_bvec = fname_presuffix(in_bvec, suffix="_thinned", newpath=op.abspath("."))
+    np.savetxt(out_bvec, bvec_thinned)
+
+    print("%s%s" % ('Dropping outlier volumes:\n', drop_scans))
+    return out_file, out_bval, out_bvec
+
+
+def get_params(A):
+    """This is a copy of spm's spm_imatrix where
+    we already know the rotations and translations matrix,
+    shears and zooms (as outputs from fsl FLIRT/avscale)
+    Let A = the 4x4 rotation and translation matrix
+    R = [          c5*c6,           c5*s6, s5]
+        [-s4*s5*c6-c4*s6, -s4*s5*s6+c4*c6, s4*c5]
+        [-c4*s5*c6+s4*s6, -c4*s5*s6-s4*c6, c4*c5]
+    """
+
+    def rang(b):
+        a = min(max(b, -1), 1)
+        return a
+
+    Ry = np.arcsin(A[0, 2])
+    # Rx = np.arcsin(A[1, 2] / np.cos(Ry))
+    # Rz = np.arccos(A[0, 1] / np.sin(Ry))
+
+    if (abs(Ry) - np.pi / 2) ** 2 < 1e-9:
+        Rx = 0
+        Rz = np.arctan2(-rang(A[1, 0]), rang(-A[2, 0] / A[0, 2]))
+    else:
+        c = np.cos(Ry)
+        Rx = np.arctan2(rang(A[1, 2] / c), rang(A[2, 2] / c))
+        Rz = np.arctan2(rang(A[0, 1] / c), rang(A[0, 0] / c))
+
+    rotations = [Rx, Ry, Rz]
+    translations = [A[0, 3], A[1, 3], A[2, 3]]
+
+    return rotations, translations
+
+
+def get_flirt_motion_parameters(flirt_mats):
+    import os.path as op
+    from nipype.interfaces.fsl.utils import AvScale
+    from dmriprep.core import get_params
+
+    motion_params = open(op.abspath("motion_parameters.par"), "w")
+    for mat in flirt_mats:
+        res = AvScale(mat_file=mat).run()
+        A = np.asarray(res.outputs.rotation_translation_matrix)
+        rotations, translations = get_params(A)
+        for i in rotations + translations:
+            motion_params.write("%f " % i)
+        motion_params.write("\n")
+    motion_params.close()
+    motion_params = op.abspath("motion_parameters.par")
+    return motion_params
+
+
+def read_nifti_sidecar(json_file):
+    import json
+
+    with open(json_file, "r") as f:
+        metadata = json.load(f)
+    pe_dir = metadata["PhaseEncodingDirection"]
+    slice_times = metadata.get("SliceTiming")
+    trt = metadata.get("TotalReadoutTime")
+    if trt is None:
+        pass
+
+    return {
+        "PhaseEncodingDirection": pe_dir,
+        "SliceTiming": slice_times,
+        "TotalReadoutTime": trt,
+    }
+
+
+def extract_metadata(metadata):
+    from dmriprep.core import read_nifti_sidecar
+
+    acqp_lines = {
+        "i": "1 0 0 %.6f",
+        "j": "0 1 0 %.6f",
+        "k": "0 0 1 %.6f",
+        "i-": "-1 0 0 %.6f",
+        "j-": "0 -1 0 %.6f",
+        "k-": "0 0 -1 %.6f",
+    }
+    spec = read_nifti_sidecar(metadata)
+    spec_line = acqp_lines[spec["PhaseEncodingDirection"]]
+    spec_acqp = spec_line % spec["TotalReadoutTime"]
+    spec_slice = spec["SliceTiming"]
+    return spec_line, spec_acqp, spec_slice
+
+
+def check_shelled(gtab_file):
+    from dipy.io import load_pickle
+
+    # Check whether data is shelled
+    gtab = load_pickle(gtab_file)
+    if len(np.unique(gtab.bvals)) > 2:
+        is_shelled = True
+    else:
+        is_shelled = False
+    return is_shelled
+
+
+def make_mean_b0(in_file):
+    import time
+
+    b0_img = nib.load(in_file)
+    b0_img_data = b0_img.get_data()
+    mean_b0 = np.mean(b0_img_data, axis=3, dtype=b0_img_data.dtype)
+    mean_file_out = in_file.split(".nii.gz")[0] + "_mean.nii.gz"
+    nib.save(
+        nib.Nifti1Image(mean_b0, affine=b0_img.affine, header=b0_img.header),
+        mean_file_out,
+    )
+    while os.path.isfile(mean_file_out) is False:
+        time.sleep(1)
+    return mean_file_out
+
+
+def suppress_gibbs(in_file, sesdir):
+    from time import time
+    from dipy.denoise.gibbs import gibbs_removal
+
+    t = time()
+    img = nib.load(in_file)
+    img_data = img.get_data()
+    gibbs_corr_data = gibbs_removal(img_data)
+    print("Time taken for gibbs suppression: ", -t + time())
+    gibbs_free_file = sesdir + "/gibbs_free_data.nii.gz"
+    nib.save(
+        nib.Nifti1Image(gibbs_corr_data.astype(np.float32), img.affine, img.header),
+        gibbs_free_file,
+    )
+    return gibbs_corr_data, gibbs_free_file
+
+
+def denoise(
+    in_file,
+    sesdir,
+    gtab_file,
+    mask,
+    strategy,
+    N=4,
+    patch_radius=2,
+    smooth_factor=3,
+    tau_factor=2.3,
+    block_radius=1,
+):
+    from time import time
+    from dipy.denoise.noise_estimate import estimate_sigma
+    from dipy.denoise.pca_noise_estimate import pca_noise_estimate
+    from dipy.denoise.localpca import localpca, mppca
+    from dipy.denoise.nlmeans import nlmeans
+    from dipy.io import load_pickle
+
+    gtab = load_pickle(gtab_file)
+    t = time()
+    img = nib.load(in_file)
+    img_data = img.get_data()
+    if strategy == "mppca":
+        img_data_den = mppca(img_data, patch_radius=patch_radius)
+    elif strategy == "localpca":
+        sigma = pca_noise_estimate(
+            img_data, gtab, correct_bias=True, smooth=smooth_factor
+        )
+        img_data_den = localpca(
+            img_data, sigma, tau_factor=tau_factor, patch_radius=patch_radius
+        )
+    elif strategy == "nlmeans":
+        sigma = estimate_sigma(img_data, N=N)
+        img_data_den = nlmeans(
+            img_data,
+            sigma=sigma,
+            mask=mask,
+            patch_radius=patch_radius,
+            block_radius=block_radius,
+            rician=True,
+        )
+    else:
+        raise ValueError("Denoising strategy not recognized.")
+    print("Time taken for denoising: ", -t + time())
+    denoised_file = sesdir + "/preprocessed_data_denoised_" + strategy + ".nii.gz"
+    nib.save(
+        nib.Nifti1Image(img_data_den.astype(np.float32), img.affine, img.header),
+        denoised_file,
+    )
+    return img_data_den, denoised_file
diff --git a/dmriprep/data.py b/dmriprep/data.py
index d06767e..7f1a3d7 100644
--- a/dmriprep/data.py
+++ b/dmriprep/data.py
@@ -16,7 +16,6 @@
 from dask.diagnostics import ProgressBar
 from tqdm.auto import tqdm
 
-
 mod_logger = logging.getLogger(__name__)
 
 
@@ -179,12 +178,13 @@ def _cumulative_paths(path_parts, add_ext=""):
     except IndexError:
         pass
 
-    return [''.join(path_parts[:i+1]) + add_ext
+    return [''.join(path_parts[:i + 1]) + add_ext
             for i in range(len(path_parts))]
 
 
 class Study:
     """A dMRI based study with a BIDS compliant directory structure"""
+
     def __init__(self, study_id, bucket, s3_prefix, subjects=None):
         """Initialize a Study instance
 
@@ -293,7 +293,6 @@ def __init__(self, study_id, bucket, s3_prefix, subjects=None):
         else:
             self._n_discarded = len([s for s in subjects if not s.valid])
 
-
     @property
     def study_id(self):
         """An identifier string for the study"""
@@ -391,6 +390,7 @@ class S3BidsStudy(Study):
     """
 
     """
+
     def __init__(self, study_id, bucket, s3_prefix=None,
                  subjects=None):
         """
@@ -427,8 +427,6 @@ def list_all_subjects(self):
         # XXX Ariel will figure this out.
 
 
-
-
 class HBN(Study):
     """The HBN study
 
@@ -436,6 +434,7 @@ class HBN(Study):
     --------
     dmriprep.data.Study
     """
+
     def __init__(self, subjects=None):
         """Initialize the HBN instance
 
@@ -463,6 +462,7 @@ def list_all_subjects(self):
         dict
             dict with participant_id as keys and site_id as values
         """
+
         def get_site_tsv_keys(site_id):
             pre = 'data/Projects/HBN/MRI/'
             raw = pre + f'{site_id}/participants.tsv'
@@ -568,6 +568,7 @@ def postprocess(self, subject):
 
 class Subject:
     """A single dMRI study subject"""
+
     def __init__(self, subject_id, study, site=None):
         """Initialize a Subject instance
 
diff --git a/dmriprep/dmriprep.py b/dmriprep/dmriprep.py
index 47911d9..0e30d86 100644
--- a/dmriprep/dmriprep.py
+++ b/dmriprep/dmriprep.py
@@ -3,11 +3,5 @@
 """Main module."""
 
 import logging
-import os
-import os.path as op
-import subprocess
-
-from .run import run_dmriprep
-
 
 mod_logger = logging.getLogger(__name__)
diff --git a/dmriprep/eddy_params.json b/dmriprep/eddy_params.json
new file mode 100644
index 0000000..631aad8
--- /dev/null
+++ b/dmriprep/eddy_params.json
@@ -0,0 +1,19 @@
+{
+  "flm": "linear",
+  "slm": "linear",
+  "fep": false,
+  "interp": "spline",
+  "nvoxhp": 1000,
+  "fudge_factor": 10,
+  "dont_sep_offs_move": false,
+  "dont_peas": false,
+  "niter": 5,
+  "method": "jac",
+  "repol": true,
+  "num_threads": 1,
+  "is_shelled": true,
+  "use_cuda": false,
+  "cnr_maps": true,
+  "residuals": false,
+  "output_type": "NIFTI_GZ"
+}
diff --git a/dmriprep/interfaces.py b/dmriprep/interfaces.py
new file mode 100644
index 0000000..1458735
--- /dev/null
+++ b/dmriprep/interfaces.py
@@ -0,0 +1,120 @@
+import os
+import os.path as op
+
+from nipype.interfaces import fsl
+from nipype.interfaces.base import isdefined
+
+
+class ExtendedEddyOutputSpec(fsl.epi.EddyOutputSpec):
+    from nipype.interfaces.base import File
+
+    shell_PE_translation_parameters = File(
+        exists=True,
+        desc="the translation along the PE-direction between the different shells",
+    )
+    outlier_map = File(
+        exists=True,
+        desc="All numbers are either 0, meaning that scan-slice "
+        "is not an outliers, or 1 meaning that it is.",
+    )
+    outlier_n_stdev_map = File(
+        exists=True,
+        desc="how many standard deviations off the mean difference "
+        "between observation and prediction is.",
+    )
+    outlier_n_sqr_stdev_map = File(
+        exists=True,
+        desc="how many standard deviations off the square root of the "
+        "mean squared difference between observation and prediction is.",
+    )
+    outlier_free_data = File(
+        exists=True,
+        desc=" the original data given by --imain not corrected for "
+        "susceptibility or EC-induced distortions or subject movement, but with "
+        "outlier slices replaced by the Gaussian Process predictions.",
+    )
+
+
+class ExtendedEddy(fsl.Eddy):
+    output_spec = ExtendedEddyOutputSpec
+    _num_threads = 1
+
+    def __init__(self, **inputs):
+        super(fsl.Eddy, self).__init__(**inputs)
+        self.inputs.on_trait_change(self._num_threads_update, "num_threads")
+        if not isdefined(self.inputs.num_threads):
+            self.inputs.num_threads = self._num_threads
+        else:
+            self._num_threads_update()
+        self.inputs.on_trait_change(self._use_cuda, "use_cuda")
+        if isdefined(self.inputs.use_cuda):
+            self._use_cuda()
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs["out_corrected"] = os.path.abspath("%s.nii.gz" % self.inputs.out_base)
+        outputs["out_parameter"] = os.path.abspath(
+            "%s.eddy_parameters" % self.inputs.out_base
+        )
+
+        # File generation might depend on the version of EDDY
+        out_rotated_bvecs = os.path.abspath(
+            "%s.eddy_rotated_bvecs" % self.inputs.out_base
+        )
+        out_movement_rms = os.path.abspath(
+            "%s.eddy_movement_rms" % self.inputs.out_base
+        )
+        out_restricted_movement_rms = os.path.abspath(
+            "%s.eddy_restricted_movement_rms" % self.inputs.out_base
+        )
+        out_shell_alignment_parameters = os.path.abspath(
+            "%s.eddy_post_eddy_shell_alignment_parameters" % self.inputs.out_base
+        )
+        shell_PE_translation_parameters = op.abspath(
+            "%s.eddy_post_eddy_shell_PE_translation_parameters" % self.inputs.out_base
+        )
+        out_outlier_report = os.path.abspath(
+            "%s.eddy_outlier_report" % self.inputs.out_base
+        )
+        outlier_map = op.abspath("%s.eddy_outlier_map" % self.inputs.out_base)
+        outlier_n_stdev_map = op.abspath(
+            "%s.eddy_outlier_n_stdev_map" % self.inputs.out_base
+        )
+        outlier_n_sqr_stdev_map = op.abspath(
+            "%s.eddy_outlier_n_sqr_stdev_map" % self.inputs.out_base
+        )
+
+        if isdefined(self.inputs.cnr_maps) and self.inputs.cnr_maps:
+            out_cnr_maps = os.path.abspath(
+                "%s.eddy_cnr_maps.nii.gz" % self.inputs.out_base
+            )
+            if os.path.exists(out_cnr_maps):
+                outputs["out_cnr_maps"] = out_cnr_maps
+        if isdefined(self.inputs.residuals) and self.inputs.residuals:
+            out_residuals = os.path.abspath(
+                "%s.eddy_residuals.nii.gz" % self.inputs.out_base
+            )
+            if os.path.exists(out_residuals):
+                outputs["out_residuals"] = out_residuals
+
+        if os.path.exists(out_rotated_bvecs):
+            outputs["out_rotated_bvecs"] = out_rotated_bvecs
+        if os.path.exists(out_movement_rms):
+            outputs["out_movement_rms"] = out_movement_rms
+        if os.path.exists(out_restricted_movement_rms):
+            outputs["out_restricted_movement_rms"] = out_restricted_movement_rms
+        if os.path.exists(out_shell_alignment_parameters):
+            outputs["out_shell_alignment_parameters"] = out_shell_alignment_parameters
+        if os.path.exists(out_outlier_report):
+            outputs["out_outlier_report"] = out_outlier_report
+
+        if op.exists(shell_PE_translation_parameters):
+            outputs["shell_PE_translation_parameters"] = shell_PE_translation_parameters
+        if op.exists(outlier_map):
+            outputs["outlier_map"] = outlier_map
+        if op.exists(outlier_n_stdev_map):
+            outputs["outlier_n_stdev_map"] = outlier_n_stdev_map
+        if op.exists(outlier_n_sqr_stdev_map):
+            outputs["outlier_n_sqr_stdev_map"] = outlier_n_sqr_stdev_map
+
+        return outputs
diff --git a/dmriprep/io.py b/dmriprep/io.py
index a154387..aa5e0c3 100644
--- a/dmriprep/io.py
+++ b/dmriprep/io.py
@@ -9,6 +9,8 @@
 import bids
 
 
+# TODO: Update the below and replace with get_bids_layout. Will need to be able to fetch data from multiple runs for
+#  separate AP/PA acquisitions and for discretized multishell acquisitions (e.g. HCP)
 def get_bids_subject_input_files(subject_id, bids_input_directory):
     """
     Function to return the needed files for dmriprep based on subject id and a bids directory.
@@ -51,14 +53,14 @@ def get_bids_subject_input_files(subject_id, bids_input_directory):
     bvec_file = [d.path for d in dwi_files if d.filename.endswith('.bvec')]
     assert len(bvec_file) == 1, 'found {} bvec files and we need just 1'.format(len(bvec_file))
 
-    subjects_dir = op.join(bids_input_directory, 'derivatives', 'sub-'+subject_id)
+    subjects_dir = op.join(bids_input_directory, 'derivatives', 'sub-' + subject_id)
 
     if not op.exists(op.join(subjects_dir, 'freesurfer')):
         raise NotImplementedError('we have not yet implemented a version of dmriprep that runs freesurfer for you.'
                                   'please run freesurfer and try again'
                                   )
 
-    outputs = dict(subject_id="sub-"+subject_id,
+    outputs = dict(subject_id="sub-" + subject_id,
                    dwi_file=dwi_file[0],
                    dwi_file_AP=ap_file[0].path,
                    dwi_file_PA=pa_file[0].path,
@@ -82,3 +84,56 @@ def get_bids_files(subject_id, bids_input_directory):
         return [get_bids_subject_input_files(sub, bids_input_directory) for sub in subjects]
     else:
         return [get_bids_subject_input_files(subject_id, bids_input_directory)]
+
+
+def get_bids_layout(bdir, subj=None, sesh=None):
+    from dmriprep.utils import merge_dicts
+    import bids
+    layout = bids.BIDSLayout(bdir, validate=False)
+    # get all files matching the specific modality we are using
+    if not subj:
+        # list of all the subjects
+        subjs = layout.get_subjects()
+    else:
+        # make it a list so we can iterate
+        subjs = [subj]
+        assert subj in subjs, "subject {} is not in the bids folder".format(subj)
+    for sub in subjs:
+        if not sesh:
+            seshs = layout.get_sessions(subject=sub, derivatives=False)
+            # in case there are non-session level inputs
+            seshs += [None]
+        else:
+            # make a list so we can iterate
+            seshs = [sesh]
+        print('\n')
+        print("%s%s" % ('Subject:', sub))
+        print("%s%s" % ('Sessions:', seshs))
+        print('\n')
+        # all the combinations of sessions and tasks that are possible
+        sub_dict = dict()
+        for ses in seshs:
+            # the attributes for our modality img
+            mod_attributes = [sub, ses]
+            # the keys for our modality img
+            mod_keys = ['subject', 'session']
+            # our query we will use for each modality img
+            mod_query = {'modality': 'dwi'}
+
+            for attr, key in zip(mod_attributes, mod_keys):
+                if attr:
+                    mod_query[key] = attr
+
+            dwi = layout.get(**merge_dicts(mod_query, {'extensions': 'nii.gz|nii'}))
+            bval = layout.get(**merge_dicts(mod_query, {'extensions': 'bval'}))
+            bvec = layout.get(**merge_dicts(mod_query, {'extensions': 'bvec'}))
+            jso = layout.get(**merge_dicts(mod_query, {'extensions': 'json'}))
+
+            sub_dict[ses] = {}
+            sub_dict[ses] = {}
+            sub_dict[ses]['dwi'] = dwi[0][0]
+            sub_dict[ses]['bval'] = bval[0][0]
+            sub_dict[ses]['bvec'] = bvec[0][0]
+            sub_dict[ses]['metadata'] = jso[0][0]
+
+    return sub_dict
diff --git a/dmriprep/qc.py b/dmriprep/qc.py
index b6663f2..8e8774b 100644
--- a/dmriprep/qc.py
+++ b/dmriprep/qc.py
@@ -1,32 +1,276 @@
 import base64
-import os.path as op
-from io import BytesIO
 
 import matplotlib
-matplotlib.use('agg')
+
+from io import BytesIO
+
+matplotlib.use("agg")
 import matplotlib.pyplot as plt
 import nibabel as nib
 import numpy as np
 
 from dipy.segment.mask import median_otsu
-from nipype.utils.filemanip import save_json, load_json
 
 
-def reorient_array(data, aff):
-    # rearrange the matrix to RAS orientation
-    orientation = nib.orientations.io_orientation(aff)
-    data_RAS = nib.orientations.apply_orientation(data, orientation)
-    # In RAS
-    return nib.orientations.apply_orientation(
-        data_RAS,
-        nib.orientations.axcodes2ornt("IPL")
-    )
+def normalize_xform(img):
+    """ Set identical, valid qform and sform matrices in an image
+    Selects the best available affine (sform > qform > shape-based), and
+    coerces it to be qform-compatible (no shears).
+    The resulting image represents this same affine as both qform and sform,
+    and is marked as NIFTI_XFORM_ALIGNED_ANAT, indicating that it is valid,
+    not aligned to template, and not necessarily preserving the original
+    coordinates.
+    If header would be unchanged, returns input image.
+    """
+    # Let nibabel convert from affine to quaternions, and recover xform
+    tmp_header = img.header.copy()
+    tmp_header.set_qform(img.affine)
+    xform = tmp_header.get_qform()
+    xform_code = 2
+
+    # Check desired codes
+    qform, qform_code = img.get_qform(coded=True)
+    sform, sform_code = img.get_sform(coded=True)
+    if all(
+        (
+            qform is not None and np.allclose(qform, xform),
+            sform is not None and np.allclose(sform, xform),
+            int(qform_code) == xform_code,
+            int(sform_code) == xform_code,
+        )
+    ):
+        return img
+
+    new_img = img.__class__(img.get_data(), xform, img.header)
+    # Unconditionally set sform/qform
+    new_img.set_sform(xform, xform_code)
+    new_img.set_qform(xform, xform_code)
+
+    return new_img
+
+
+def reorient_dwi(dwi_prep, bvecs, out_dir):
+    """
+    A function to reorient any dwi image and associated bvecs to RAS+.
+
+    Parameters
+    ----------
+    dwi_prep : str
+        File path to a dwi Nifti1Image.
+    bvecs : str
+        File path to corresponding bvecs file.
+    out_dir : str
+        Path to output directory.
+
+    Returns
+    -------
+    out_fname : str
+        File path to the reoriented dwi Nifti1Image.
+    out_bvec_fname : str
+        File path to corresponding reoriented bvecs file.
+    """
+    from dmriprep.qc import normalize_xform
+
+    fname = dwi_prep
+    bvec_fname = bvecs
+    out_bvec_fname = "%s%s" % (out_dir, "/bvecs_reor.bvec")
+
+    input_img = nib.load(fname)
+    input_axcodes = nib.aff2axcodes(input_img.affine)
+    reoriented = nib.as_closest_canonical(input_img)
+    normalized = normalize_xform(reoriented)
+    # Is the input image oriented how we want?
+    new_axcodes = ("R", "A", "S")
+    if normalized is not input_img:
+        out_fname = "%s%s%s%s" % (
+            out_dir,
+            "/",
+            dwi_prep.split("/")[-1].split(".nii.gz")[0],
+            "_reor_RAS.nii.gz",
+        )
+        print("%s%s%s" % ("Reorienting ", dwi_prep, " to RAS+..."))
+
+        # Flip the bvecs
+        input_orientation = nib.orientations.axcodes2ornt(input_axcodes)
+        desired_orientation = nib.orientations.axcodes2ornt(new_axcodes)
+        transform_orientation = nib.orientations.ornt_transform(
+            input_orientation, desired_orientation
+        )
+        bvec_array = np.loadtxt(bvec_fname)
+        if bvec_array.shape[0] != 3:
+            bvec_array = bvec_array.T
+        if not bvec_array.shape[0] == transform_orientation.shape[0]:
+            raise ValueError("Unrecognized bvec format")
+        output_array = np.zeros_like(bvec_array)
+        for this_axnum, (axnum, flip) in enumerate(transform_orientation):
+            output_array[this_axnum] = bvec_array[int(axnum)] * float(flip)
+        np.savetxt(out_bvec_fname, output_array, fmt="%.8f ")
+    else:
+        out_fname = "%s%s%s%s" % (
+            out_dir,
+            "/",
+            dwi_prep.split("/")[-1].split(".nii.gz")[0],
+            "_noreor_RAS.nii.gz",
+        )
+        out_bvec_fname = bvec_fname
+
+    normalized.to_filename(out_fname)
+
+    return out_fname, out_bvec_fname
+
+
+def reorient_img(img, out_dir):
+    """
+    A function to reorient any non-dwi image to RAS+.
+
+    Parameters
+    ----------
+    img : str
+        File path to a Nifti1Image.
+    out_dir : str
+        Path to output directory.
+
+    Returns
+    -------
+    out_name : str
+        File path to reoriented Nifti1Image.
+    """
+    from dmriprep.qc import normalize_xform
+
+    # Load image, orient as RAS
+    orig_img = nib.load(img)
+    reoriented = nib.as_closest_canonical(orig_img)
+    normalized = normalize_xform(reoriented)
+
+    # Image may be reoriented
+    if normalized is not orig_img:
+        print("%s%s%s" % ("Reorienting ", img, " to RAS+..."))
+        out_name = "%s%s%s%s" % (
+            out_dir,
+            "/",
+            img.split("/")[-1].split(".nii.gz")[0],
+            "_reor_RAS.nii.gz",
+        )
+    else:
+        out_name = "%s%s%s%s" % (
+            out_dir,
+            "/",
+            img.split("/")[-1].split(".nii.gz")[0],
+            "_noreor_RAS.nii.gz",
+        )
+
+    normalized.to_filename(out_name)
+
+    return out_name
+
+
+def match_target_vox_res(img_file, vox_size, out_dir):
+    """
+    A function to resample an image to a given isotropic voxel resolution.
+
+    Parameters
+    ----------
+    img_file : str
+        File path to a Nifti1Image.
+    vox_size : str
+        Voxel size in mm. (e.g. 2mm).
+    out_dir : str
+        Path to output directory.
+
+    Returns
+    -------
+    img_file : str
+        File path to resampled Nifti1Image.
+    """
+    import os
+    from dipy.align.reslice import reslice
+
+    # Check dimensions
+    img = nib.load(img_file)
+    data = img.get_fdata()
+    affine = img.affine
+    hdr = img.header
+    zooms = hdr.get_zooms()[:3]
+    if vox_size == "1mm":
+        new_zooms = (1.0, 1.0, 1.0)
+    elif vox_size == "2mm":
+        new_zooms = (2.0, 2.0, 2.0)
+
+    if (abs(zooms[0]), abs(zooms[1]), abs(zooms[2])) != new_zooms:
+        print("Reslicing image " + img_file + " to " + vox_size + "...")
+        img_file_res = "%s%s%s%s%s%s" % (
+            out_dir,
+            "/",
+            os.path.basename(img_file).split(".nii.gz")[0],
+            "_res",
+            vox_size,
+            ".nii.gz",
+        )
+        data2, affine2 = reslice(data, affine, zooms, new_zooms)
+        img2 = nib.Nifti1Image(data2, affine=affine2)
+        nib.save(img2, img_file_res)
+        img_file = img_file_res
+    else:
+        img_file_nores = "%s%s%s%s%s%s" % (
+            out_dir,
+            "/",
+            os.path.basename(img_file).split(".nii.gz")[0],
+            "_nores",
+            vox_size,
+            ".nii.gz",
+        )
+        nib.save(img, img_file_nores)
+        img_file = img_file_nores
+
+    return img_file
+
+
+def check_orient_and_dims(infile, vox_size, bvecs, outdir, overwrite=True):
+    """
+    An API to reorient any image to RAS+ and resample any image to a given voxel resolution.
+
+    Parameters
+    ----------
+    infile : str
+        File path to a dwi Nifti1Image.
+    vox_size : str
+        Voxel size in mm. (e.g. 2mm).
+    bvecs : str
+        File path to corresponding bvecs file if infile is a dwi.
+    outdir : str
+        Path to output directory.
+    overwrite : bool
+        Boolean indicating whether to overwrite existing outputs. Default is True.
+
+    Returns
+    -------
+    outfile : str
+        File path to the reoriented and/or resample Nifti1Image.
+    bvecs : str
+        File path to corresponding reoriented bvecs file if outfile is a dwi.
+    """
+    import warnings
+
+    warnings.filterwarnings("ignore")
+    from dmriprep.qc import reorient_dwi, match_target_vox_res
+
+    # Check orientation
+    # dwi case
+    # Check orientation
+    if ("RAS" not in infile) or (overwrite is True):
+        [infile, bvecs] = reorient_dwi(infile, bvecs, outdir)
+    # Check dimensions
+    if ("reor" not in infile) or (overwrite is True):
+        outfile = match_target_vox_res(infile, vox_size, outdir)
+        print(outfile)
+
+    return outfile, bvecs
 
 
 def mplfig(data, outfile=None, as_bytes=False):
     fig = plt.figure(frameon=False, dpi=data.shape[0])
-    fig.set_size_inches(float(data.shape[1])/data.shape[0], 1)
-    ax = plt.Axes(fig, [0., 0., 1., 1.])
+    fig.set_size_inches(float(data.shape[1]) / data.shape[0], 1)
+    ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
     ax.set_axis_off()
     fig.add_axes(ax)
     ax.imshow(data, aspect=1, cmap=plt.cm.Greys_r)  # previous aspect="normal"
@@ -36,7 +280,7 @@ def mplfig(data, outfile=None, as_bytes=False):
         return outfile
     if as_bytes:
         IObytes = BytesIO()
-        plt.savefig(IObytes, format='png', dpi=data.shape[0], transparent=True)
+        plt.savefig(IObytes, format="png", dpi=data.shape[0], transparent=True)
         IObytes.seek(0)
         base64_jpgData = base64.b64encode(IObytes.read())
         return base64_jpgData.decode("ascii")
@@ -44,8 +288,8 @@ def mplfig(data, outfile=None, as_bytes=False):
 
 def mplfigcontour(data, outfile=None, as_bytes=False):
     fig = plt.figure(frameon=False)
-    fig.set_size_inches(float(data.shape[1])/data.shape[0], 1)
-    ax = plt.Axes(fig, [0., 0., 1., 1.])
+    fig.set_size_inches(float(data.shape[1]) / data.shape[0], 1)
+    ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
     ax.set_axis_off()
     fig.add_axes(ax)
 
@@ -59,45 +303,49 @@ def mplfigcontour(data, outfile=None, as_bytes=False):
         return outfile
     if as_bytes:
         IObytes = BytesIO()
-        plt.savefig(IObytes, format='png', dpi=data.shape[0], transparent=True)
+        plt.savefig(IObytes, format="png", dpi=data.shape[0], transparent=True)
         IObytes.seek(0)
         base64_jpgData = base64.b64encode(IObytes.read())
         return base64_jpgData.decode("ascii")
 
 
-def load_and_reorient(filename):
-    img = nib.load(filename)
-    data, aff = img.get_data(), img.affine
-    data = reorient_array(data, aff)
-    return data
-
-
 def reshape3D(data, n=256):
-    return np.pad(data, (
+    return np.pad(
+        data,
         (
-            (n-data.shape[0]) // 2,
-            ((n-data.shape[0]) + (data.shape[0] % 2 > 0)) // 2
+            (
+                (n - data.shape[0]) // 2,
+                ((n - data.shape[0]) + (data.shape[0] % 2 > 0)) // 2,
+            ),
+            (
+                (n - data.shape[1]) // 2,
+                ((n - data.shape[1]) + (data.shape[1] % 2 > 0)) // 2,
+            ),
+            (0, 0),
         ),
-        (
-            (n-data.shape[1]) // 2,
-            ((n-data.shape[1]) + (data.shape[1] % 2 > 0)) // 2
-        ),
-        (0, 0)
-    ), "constant", constant_values=(0, 0))
+        "constant",
+        constant_values=(0, 0),
+    )
 
 
 def reshape4D(data, n=256):
-    return np.pad(data, (
+    return np.pad(
+        data,
         (
-            (n-data.shape[0]) // 2,
-            ((n-data.shape[0]) + (data.shape[0] % 2 > 0)) // 2
+            (
+                (n - data.shape[0]) // 2,
+                ((n - data.shape[0]) + (data.shape[0] % 2 > 0)) // 2,
+            ),
+            (
+                (n - data.shape[1]) // 2,
+                ((n - data.shape[1]) + (data.shape[1] % 2 > 0)) // 2,
+            ),
+            (0, 0),
+            (0, 0),
         ),
-        (
-            (n-data.shape[1]) // 2,
-            ((n-data.shape[1]) + (data.shape[1] % 2 > 0)) // 2
-        ),
-        (0, 0), (0, 0)
-    ), "constant", constant_values=(0, 0))
+        "constant",
+        constant_values=(0, 0),
+    )
 
 
 def get_middle_slices(data, slice_direction):
@@ -117,7 +365,7 @@ def get_middle_slices(data, slice_direction):
 
 def nearest_square(limit):
     answer = 0
-    while (answer+1)**2 < limit:
+    while (answer + 1) ** 2 < limit:
         answer += 1
     if (answer ** 2) == limit:
         return answer
@@ -128,17 +376,17 @@ def nearest_square(limit):
 def create_sprite_from_tiles(tile, out_file=None, as_bytes=False):
     num_slices = tile.shape[-1]
     N = nearest_square(num_slices)
-    M = int(np.ceil(num_slices/N))
+    M = int(np.ceil(num_slices / N))
     # tile is square, so just make a big arr
     pix = tile.shape[0]
 
     if len(tile.shape) == 3:
-        mosaic = np.zeros((N*tile.shape[0], M*tile.shape[0]))
+        mosaic = np.zeros((N * tile.shape[0], M * tile.shape[0]))
     else:
-        mosaic = np.zeros((N*tile.shape[0], M*tile.shape[0], tile.shape[-2]))
+        mosaic = np.zeros((N * tile.shape[0], M * tile.shape[0], tile.shape[-2]))
 
     mosaic[:] = np.nan
-    helper = np.arange(N*M).reshape((N, M))
+    helper = np.arange(N * M).reshape((N, M))
 
     for t in range(num_slices):
         x, y = np.nonzero(helper == t)
@@ -163,7 +411,6 @@ def create_sprite_from_tiles(tile, out_file=None, as_bytes=False):
 
 
 def createSprite4D(dwi_file):
-
     # initialize output dict
     output = []
 
@@ -171,13 +418,13 @@ def createSprite4D(dwi_file):
     dwi = load_and_reorient(dwi_file)[:, :, :, 1:]
 
     # create tiles from center slice on each orientation
-    for orient in ['sag', 'ax', 'cor']:
+    for orient in ["sag", "ax", "cor"]:
         tile = get_middle_slices(dwi, orient)
 
         # create sprite images for each
         results = create_sprite_from_tiles(tile, as_bytes=True)
-        results['img_type'] = '4dsprite'
-        results['orientation'] = orient
+        results["img_type"] = "4dsprite"
+        results["orientation"] = orient
         output.append(results)
 
     return output
@@ -194,45 +441,45 @@ def createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file):
     b0 = reshape3D(b0, N)
     _, mask = median_otsu(b0)
     outb0 = create_sprite_from_tiles(b0, as_bytes=True)
-    outb0['img_type'] = 'brainsprite'
+    outb0["img_type"] = "brainsprite"
 
     # make a colorFA sprite, masked by b0
     Q = reshape4D(colorfa, N)
     Q[np.logical_not(mask)] = np.nan
-    Q = np.moveaxis(Q,  -2, -1)
+    Q = np.moveaxis(Q, -2, -1)
     outcolorFA = create_sprite_from_tiles(Q, as_bytes=True)
-    outcolorFA['img_type'] = 'brainsprite'
+    outcolorFA["img_type"] = "brainsprite"
 
     # make an anat mask contour sprite
     outmask = create_sprite_from_tiles(reshape3D(anat_mask, N))
     img = mplfigcontour(outmask.pop("mosaic"), as_bytes=True)
-    outmask['img'] = img
+    outmask["img"] = img
 
     return outb0, outcolorFA, outmask
 
 
-def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
-                       color_fa_file, anat_mask_file,
-                       outlier_indices,
-                       eddy_qc_file,
-                       outpath=op.abspath('./report.json')):
-
-    report = {}
-    report['dwi_corrected'] = createSprite4D(dwi_corrected_file)
-
-    b0, colorFA, mask = createB0_ColorFA_Mask_Sprites(dwi_corrected_file,
-                                                      color_fa_file,
-                                                      anat_mask_file)
-    report['b0'] = b0
-    report['colorFA'] = colorFA
-    report['anat_mask'] = mask
-    report['outlier_volumes'] = outlier_indices.tolist()
-
-    with open(eddy_report, 'r') as f:
-        report['eddy_report'] = f.readlines()
-
-    report['eddy_params'] = np.genfromtxt(eddy_rms).tolist()
-    eddy_qc = load_json(eddy_qc_file)
-    report['eddy_quad'] = eddy_qc
-    save_json(outpath, report)
-    return outpath
+# def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
+#                        color_fa_file, anat_mask_file,
+#                        outlier_indices,
+#                        eddy_qc_file,
+#                        outpath=op.abspath('./report.json')):
+#
+#     report = {}
+#     report['dwi_corrected'] = createSprite4D(dwi_corrected_file)
+#
+#     b0, colorFA, mask = createB0_ColorFA_Mask_Sprites(dwi_corrected_file,
+#                                                       color_fa_file,
+#                                                       anat_mask_file)
+#     report['b0'] = b0
+#     report['colorFA'] = colorFA
+#     report['anat_mask'] = mask
+#     report['outlier_volumes'] = outlier_indices.tolist()
+#
+#     with open(eddy_report, 'r') as f:
+#         report['eddy_report'] = f.readlines()
+#
+#     report['eddy_params'] = np.genfromtxt(eddy_rms).tolist()
+#     eddy_qc = load_json(eddy_qc_file)
+#     report['eddy_quad'] = eddy_qc
+#     save_json(outpath, report)
+#     return outpath
diff --git a/dmriprep/run.py b/dmriprep/run.py
index 9ac70d8..6a3c180 100644
--- a/dmriprep/run.py
+++ b/dmriprep/run.py
@@ -1,855 +1,422 @@
 import os
-import os.path as op
-from shutil import copyfile
 
 
-def run_dmriprep(dwi_file, bvec_file, bval_file,
-                 subjects_dir, working_dir, out_dir):
+def init_single_subject_wf(
+    sub,
+    ses,
+    dwi,
+    fbval,
+    fbvec,
+    metadata,
+    out_dir,
+    strategy="mppca",
+    vox_size="2mm",
+    plugin_type="MultiProc",
+    outlier_thresh=0.10,
+    verbose=False
+):
+    import json
+    from pathlib import Path
+    from nipype.pipeline import engine as pe
+    from nipype.interfaces import utility as niu
+    from nipype.interfaces import fsl
+    from nipype.algorithms.rapidart import ArtifactDetect
+    from dmriprep import interfaces, core, qc
+
+    import_list = [
+        "import sys",
+        "import os",
+        "import numpy as np",
+        "import nibabel as nib",
+        "import warnings",
+        'warnings.filterwarnings("ignore")',
+    ]
 
-    """
-    Runs dmriprep for acquisitions with just one PE direction.
+    subdir = "%s%s%s" % (out_dir, "/", sub)
+    if not os.path.isdir(subdir):
+        os.mkdir(subdir)
+    sesdir = "%s%s%s%s%s" % (out_dir, "/", sub, "/ses-", ses)
+    if not os.path.isdir(sesdir):
+        os.mkdir(sesdir)
+
+    eddy_cfg_file = "%s%s" % (str(Path(__file__).parent), "/eddy_params.json")
+    topup_config_odd = "%s%s" % (str(Path(__file__).parent), "/b02b0_1.cnf")
+
+    # Create dictionary of eddy args
+    with open(eddy_cfg_file, "r") as f:
+        eddy_args = json.load(f)
+
+    wf = pe.Workflow(name="single_subject_dmri")
+    wf.base_dir = sesdir
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=[
+                "dwi",
+                "fbvec",
+                "fbval",
+                "metadata",
+                "sub",
+                "ses",
+                "sesdir",
+                "strategy",
+                "vox_size",
+                "outlier_thresh",
+                "eddy_cfg_file",
+                "topup_config_odd",
+            ]
+        ),
+        name="inputnode",
+    )
+    inputnode.inputs.dwi = dwi
+    inputnode.inputs.fbvec = fbvec
+    inputnode.inputs.fbval = fbval
+    inputnode.inputs.metadata = metadata
+    inputnode.inputs.sub = sub
+    inputnode.inputs.ses = ses
+    inputnode.inputs.sesdir = sesdir
+    inputnode.inputs.strategy = strategy
+    inputnode.inputs.vox_size = vox_size
+    inputnode.inputs.outlier_thresh = outlier_thresh
+    inputnode.inputs.eddy_cfg_file = eddy_cfg_file
+    inputnode.inputs.topup_config_odd = topup_config_odd
+
+    check_orient_and_dims_dwi_node = pe.Node(
+        niu.Function(
+            input_names=["infile", "vox_size", "bvecs", "outdir"],
+            output_names=["outfile", "bvecs"],
+            function=qc.check_orient_and_dims,
+            imports=import_list,
+        ),
+        name="check_orient_and_dims_dwi_node",
+    )
 
-    """
-    from glob import glob
-    import nibabel as nib
-    import nipype.interfaces.freesurfer as fs
-    import nipype.interfaces.fsl as fsl
-    import nipype.interfaces.io as nio
-    import nipype.interfaces.utility as niu
-    import nipype.pipeline.engine as pe
-    import numpy as np
-    from nipype.algorithms.rapidart import ArtifactDetect
-    from nipype.interfaces.dipy import DTI
-    from nipype.interfaces.fsl.utils import AvScale
-    from nipype.utils.filemanip import fname_presuffix
-    from nipype.workflows.dmri.fsl.epi import create_dmri_preprocessing
-
-    wf = create_dmri_preprocessing(name='dmriprep',
-                                   use_fieldmap=False,
-                                   fieldmap_registration=False)
-    wf.inputs.inputnode.ref_num = 0
-    wf.inputs.inputnode.in_file = dwi_file
-    wf.inputs.inputnode.in_bvec = bvec_file
-
-    dwi_fname = op.split(dwi_file)[1].split(".nii.gz")[0]
-    bids_sub_name = dwi_fname.split("_")[0]
-    assert bids_sub_name.startswith("sub-")
-
-    # inputnode = wf.get_node("inputnode")
-    outputspec = wf.get_node("outputnode")
-
-    # QC: FLIRT translation and rotation parameters
-    flirt = wf.get_node("motion_correct.coregistration")
-    # flirt.inputs.save_mats = True
-
-    get_tensor = pe.Node(DTI(), name="dipy_tensor")
-    wf.connect(outputspec, "dmri_corrected", get_tensor, "in_file")
-    # wf.connect(inputspec2,"bvals", get_tensor, "in_bval")
-    get_tensor.inputs.in_bval = bval_file
-    wf.connect(outputspec, "bvec_rotated", get_tensor, "in_bvec")
-
-    scale_tensor = pe.Node(name='scale_tensor', interface=fsl.BinaryMaths())
-    scale_tensor.inputs.operation = 'mul'
-    scale_tensor.inputs.operand_value = 1000
-    wf.connect(get_tensor, 'out_file', scale_tensor, 'in_file')
-
-    fslroi = pe.Node(fsl.ExtractROI(t_min=0, t_size=1), name="fslroi")
-    wf.connect(outputspec, "dmri_corrected", fslroi, "in_file")
-
-    bbreg = pe.Node(fs.BBRegister(contrast_type="t2", init="fsl",
-                                  out_fsl_file=True, subjects_dir=subjects_dir,
-                                  epi_mask=True), name="bbreg")
-    # wf.connect(inputspec2,"fsid", bbreg,"subject_id")
-    bbreg.inputs.subject_id = 'freesurfer'  # bids_sub_name
-    wf.connect(fslroi, "roi_file", bbreg, "source_file")
-
-    voltransform = pe.Node(fs.ApplyVolTransform(inverse=True),
-                           iterfield=['source_file', 'reg_file'],
-                           name='transform')
-    voltransform.inputs.subjects_dir = subjects_dir
-
-    vt2 = voltransform.clone("transform_aparcaseg")
-    vt2.inputs.interp = "nearest"
-
-    def binarize_aparc(aparc_aseg):
-        img = nib.load(aparc_aseg)
-        data, aff = img.get_data(), img.affine
-        outfile = fname_presuffix(
-            aparc_aseg, suffix="bin.nii.gz",
-            newpath=op.abspath("."), use_ext=False
-        )
-        nib.Nifti1Image((data > 0).astype(float), aff).to_filename(outfile)
-        return outfile
-
-    # wf.connect(inputspec2, "mask_nii", voltransform, "target_file")
-    create_mask = pe.Node(niu.Function(input_names=["aparc_aseg"],
-                                       output_names=["outfile"],
-                                       function=binarize_aparc),
-                          name="bin_aparc")
-
-    def get_aparc_aseg(subjects_dir, sub):
-        return op.join(subjects_dir, sub, "mri", "aparc+aseg.mgz")
-
-    create_mask.inputs.aparc_aseg = get_aparc_aseg(subjects_dir, 'freesurfer')
-    wf.connect(create_mask, "outfile", voltransform, "target_file")
-
-    wf.connect(fslroi, "roi_file", voltransform, "source_file")
-    wf.connect(bbreg, "out_reg_file", voltransform, "reg_file")
-
-    vt2.inputs.target_file = get_aparc_aseg(subjects_dir, 'freesurfer')
-    # wf.connect(inputspec2, "aparc_aseg", vt2, "target_file")
-    wf.connect(fslroi, "roi_file", vt2, "source_file")
-    wf.connect(bbreg, "out_reg_file", vt2, "reg_file")
-
-    # AK (2017): THIS NODE MIGHT NOT BE NECESSARY
-    # AK (2018) doesn't know why she said that above..
-    threshold2 = pe.Node(fs.Binarize(min=0.5, out_type='nii.gz', dilate=1),
-                         iterfield=['in_file'],
-                         name='threshold2')
-    wf.connect(voltransform, "transformed_file", threshold2, "in_file")
-
-    # wf.connect(getmotion, "motion_params", datasink, "dti.@motparams")
-
-    def get_flirt_motion_parameters(flirt_out_mats):
-        def get_params(A):
-            """This is a copy of spm's spm_imatrix where
-            we already know the rotations and translations matrix,
-            shears and zooms (as outputs from fsl FLIRT/avscale)
-            Let A = the 4x4 rotation and translation matrix
-            R = [          c5*c6,           c5*s6, s5]
-                [-s4*s5*c6-c4*s6, -s4*s5*s6+c4*c6, s4*c5]
-                [-c4*s5*c6+s4*s6, -c4*s5*s6-s4*c6, c4*c5]
-            """
-            def rang(b):
-                a = min(max(b, -1), 1)
-                return a
-            Ry = np.arcsin(A[0, 2])
-            # Rx = np.arcsin(A[1, 2] / np.cos(Ry))
-            # Rz = np.arccos(A[0, 1] / np.sin(Ry))
-
-            if (abs(Ry)-np.pi/2)**2 < 1e-9:
-                Rx = 0
-                Rz = np.arctan2(-rang(A[1, 0]), rang(-A[2, 0]/A[0, 2]))
-            else:
-                c = np.cos(Ry)
-                Rx = np.arctan2(rang(A[1, 2]/c), rang(A[2, 2]/c))
-                Rz = np.arctan2(rang(A[0, 1]/c), rang(A[0, 0]/c))
-
-            rotations = [Rx, Ry, Rz]
-            translations = [A[0, 3], A[1, 3], A[2, 3]]
-
-            return rotations, translations
-
-        motion_params = open(op.abspath('motion_parameters.par'), 'w')
-        for mat in flirt_out_mats:
-            res = AvScale(mat_file=mat).run()
-            A = np.asarray(res.outputs.rotation_translation_matrix)
-            rotations, translations = get_params(A)
-            for i in rotations+translations:
-                motion_params.write('%f ' % i)
-            motion_params.write('\n')
-        motion_params.close()
-        motion_params = op.abspath('motion_parameters.par')
-        return motion_params
-
-    getmotion = pe.Node(
-        niu.Function(input_names=["flirt_out_mats"],
-                     output_names=["motion_params"],
-                     function=get_flirt_motion_parameters),
-        name="get_motion_parameters",
-        iterfield="flirt_out_mats"
+    # Make gtab and get b0 indices
+    correct_vecs_and_make_b0s_node = pe.Node(
+        niu.Function(
+            input_names=["fbval", "fbvec", "dwi_file", "sesdir"],
+            output_names=["firstb0", "firstb0_file", "gtab_file", "b0_vols", "b0s"],
+            function=core.correct_vecs_and_make_b0s,
+            imports=import_list,
+        ),
+        name="correct_vecs_and_make_b0s",
     )
 
-    wf.connect(flirt, "out_matrix_file", getmotion, "flirt_out_mats")
-
-    art = pe.Node(interface=ArtifactDetect(), name="art")
-    art.inputs.use_differences = [True, True]
-    art.inputs.save_plot = False
-    art.inputs.use_norm = True
-    art.inputs.norm_threshold = 3
-    art.inputs.zintensity_threshold = 9
-    art.inputs.mask_type = 'spm_global'
-    art.inputs.parameter_source = 'FSL'
-
-    wf.connect(getmotion, "motion_params", art, "realignment_parameters")
-    wf.connect(outputspec, "dmri_corrected", art, "realigned_files")
-
-    datasink = pe.Node(nio.DataSink(), name="sinker")
-    datasink.inputs.base_directory = out_dir
-    datasink.inputs.substitutions = [
-        ("vol0000_flirt_merged.nii.gz", dwi_fname + '.nii.gz'),
-        ("stats.vol0000_flirt_merged.txt", dwi_fname + ".art.json"),
-        ("motion_parameters.par", dwi_fname + ".motion.txt"),
-        ("_rotated.bvec", ".bvec"),
-        ("aparc+aseg_warped_out", dwi_fname.replace("_dwi", "_aparc+aseg")),
-        ("art.vol0000_flirt_merged_outliers.txt", dwi_fname + ".outliers.txt"),
-        ("vol0000_flirt_merged", dwi_fname),
-        ("_roi_bbreg_freesurfer", "_register"),
-        ("aparc+asegbin_warped_thresh", dwi_fname.replace("_dwi", "_mask")),
-        ("derivatives/dmriprep", "derivatives/{}/dmriprep".format(bids_sub_name))
-    ]
+    btr_node_premoco = pe.Node(fsl.BET(), name="bet_pre_moco")
+    btr_node_premoco.inputs.mask = True
+    btr_node_premoco.inputs.frac = 0.2
 
-    wf.connect(art, "statistic_files", datasink, "dmriprep.art.@artstat")
-    wf.connect(art, "outlier_files", datasink, "dmriprep.art.@artoutlier")
-    wf.connect(outputspec, "dmri_corrected", datasink, "dmriprep.dwi.@corrected")
-    wf.connect(outputspec, "bvec_rotated", datasink, "dmriprep.dwi.@rotated")
-    wf.connect(getmotion, "motion_params", datasink, "dmriprep.art.@motion")
-
-    wf.connect(get_tensor, "out_file", datasink, "dmriprep.dti.@tensor")
-    wf.connect(get_tensor, "fa_file", datasink, "dmriprep.dti.@fa")
-    wf.connect(get_tensor, "md_file", datasink, "dmriprep.dti.@md")
-    wf.connect(get_tensor, "ad_file", datasink, "dmriprep.dti.@ad")
-    wf.connect(get_tensor, "rd_file", datasink, "dmriprep.dti.@rd")
-    wf.connect(get_tensor, "out_file", datasink, "dmriprep.dti.@scaled_tensor")
-
-    wf.connect(bbreg, "min_cost_file", datasink, "dmriprep.reg.@mincost")
-    wf.connect(bbreg, "out_fsl_file", datasink, "dmriprep.reg.@fslfile")
-    wf.connect(bbreg, "out_reg_file", datasink, "dmriprep.reg.@reg")
-    wf.connect(threshold2, "binary_file", datasink, "dmriprep.anat.@mask")
-    # wf.connect(vt2, "transformed_file", datasink, "dwi.@aparc_aseg")
-
-    convert = pe.Node(fs.MRIConvert(out_type="niigz"), name="convert2nii")
-    wf.connect(vt2, "transformed_file", convert, "in_file")
-    wf.connect(convert, "out_file", datasink, "dmriprep.anat.@aparc_aseg")
-
-    wf.base_dir = working_dir
-    wf.run()
-
-    copyfile(bval_file, op.join(
-        out_dir, bids_sub_name, "dmriprep", "dwi",
-        op.split(bval_file)[1]
-    ))
-
-    dmri_corrected = glob(op.join(out_dir, '*/dmriprep/dwi', '*.nii.gz'))[0]
-    bvec_rotated = glob(op.join(out_dir, '*/dmriprep/dwi', '*.bvec'))[0]
-    bval_file = glob(op.join(out_dir, '*/dmriprep/dwi', '*.bval'))[0]
-    art_file = glob(op.join(out_dir, '*/dmriprep/art', '*.art.json'))[0]
-    motion_file = glob(op.join(out_dir, '*/dmriprep/art', '*.motion.txt'))[0]
-    outlier_file = glob(op.join(out_dir, '*/dmriprep/art', '*.outliers.txt'))[0]
-    return dmri_corrected, bvec_rotated, art_file, motion_file, outlier_file
-
-
-def run_dmriprep_pe(subject_id, dwi_file, dwi_file_AP, dwi_file_PA,
-                    bvec_file, bval_file,
-                    subjects_dir, working_dir, out_dir,
-                    eddy_niter=5, slice_outlier_threshold=0.02):
-    """Run the dmriprep (phase encoded) nipype workflow
-
-    Parameters
-    ----------
-    subject_id : str
-        Subject identifier
-
-    dwi_file : str
-        Path to dwi nifti file
-
-    dwi_file_AP : str
-        Path to EPI nifti file (anterior-posterior)
-
-    dwi_file_PA : str
-        Path to EPI nifti file (posterior-anterior)
-
-    bvec_file : str
-        Path to bvec file
-
-    bval_file : str
-        Path to bval file
-
-    subjects_dir : str
-        Path to subject's freesurfer directory
-
-    working_dir : str
-        Path to workflow working directory
-
-    out_dir : str
-        Path to output directory
-
-    eddy_niter : int, default=5
-        Fixed number of eddy iterations. See
-        https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#A--niter
-
-    slice_outlier_threshold: int or float
-        Number of allowed outlier slices per volume. If this is exceeded the
-        volume is dropped from analysis. If `slice_outlier_threshold` is an
-        int, it is treated as number of allowed outlier slices. If
-        `slice_outlier_threshold` is a float between 0 and 1 (exclusive), it is
-        treated the fraction of allowed outlier slices.
-
-    Notes
-    -----
-    This assumes that there are scans with phase-encode directions AP/PA for
-    topup.
-
-    See Also
-    --------
-    dmriprep.run.get_dmriprep_pe_workflow
-    """
-    wf = get_dmriprep_pe_workflow()
-    wf.base_dir = op.join(op.abspath(working_dir), subject_id)
-
-    inputspec = wf.get_node('inputspec')
-    inputspec.inputs.subject_id = subject_id
-    inputspec.inputs.dwi_file = dwi_file
-    inputspec.inputs.dwi_file_ap = dwi_file_AP
-    inputspec.inputs.dwi_file_pa = dwi_file_PA
-    inputspec.inputs.bvec_file = bvec_file
-    inputspec.inputs.bval_file = bval_file
-    inputspec.inputs.subjects_dir = subjects_dir
-    inputspec.inputs.out_dir = op.abspath(out_dir)
-    inputspec.inputs.eddy_niter = eddy_niter
-    inputspec.inputs.slice_outlier_threshold = slice_outlier_threshold
-
-    # write the graph (this is saved to the working dir)
-    wf.write_graph()
-    wf.config['execution']['remove_unnecessary_outputs'] = False
-    wf.config['execution']['keep_inputs'] = True
-    wf.run()
-
-
-def get_dmriprep_pe_workflow():
-    """Return the dmriprep (phase encoded) nipype workflow
-
-    Parameters
-    ----------
-
-
-    Returns
-    -------
-    wf : nipype.pipeline.engine.Workflow
-        Nipype dmriprep workflow
-
-    Notes
-    -----
-    This assumes that there are scans with phase-encode directions AP/PA for
-    topup.
-    """
-    import nipype.interfaces.freesurfer as fs
-    import nipype.interfaces.fsl as fsl
-    import nipype.interfaces.io as nio
-    import nipype.interfaces.utility as niu
-    import nipype.pipeline.engine as pe
-    from nipype.interfaces.dipy import DTI
-    from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline
-
-    inputspec = pe.Node(niu.IdentityInterface(fields=[
-        'subject_id',
-        'dwi_file',
-        'dwi_file_ap',
-        'dwi_file_pa',
-        'bvec_file',
-        'bval_file',
-        'subjects_dir',
-        'out_dir',
-        'eddy_niter',
-        'slice_outlier_threshold'
-    ]), name="inputspec")
-
-    # AK: watch out, other datasets might be encoded LR
-    epi_ap = {'echospacing': 66.5e-3, 'enc_dir': 'y-'}
-    epi_pa = {'echospacing': 66.5e-3, 'enc_dir': 'y'}
-    prep = all_fsl_pipeline(epi_params=epi_ap, altepi_params=epi_pa)
-
-    # initialize an overall workflow
-    wf = pe.Workflow(name="dmriprep")
-
-    wf.connect(inputspec, 'dwi_file', prep, 'inputnode.in_file')
-    wf.connect(inputspec, 'bvec_file', prep, 'inputnode.in_bvec')
-    wf.connect(inputspec, 'bval_file', prep, 'inputnode.in_bval')
-    wf.connect(inputspec, 'eddy_niter', prep, 'fsl_eddy.niter')
-
-    eddy = prep.get_node('fsl_eddy')
-    eddy.inputs.repol = True
-    eddy.inputs.cnr_maps = True
-    eddy.inputs.residuals = True
-    import multiprocessing
-    eddy.inputs.num_threads = multiprocessing.cpu_count()
-    import numba.cuda
-    try:
-        if numba.cuda.gpus:
-            eddy.inputs.use_cuda = True
-    except:
-        eddy.inputs.use_cuda = False
-
-    topup = prep.get_node('peb_correction.topup')
-    topup.inputs.checksize = True
-
-    applytopup = prep.get_node('peb_correction.unwarp')
-    applytopup.inputs.checksize = True
-
-    eddy.inputs.checksize = True
-
-    eddy_quad = pe.Node(fsl.EddyQuad(verbose=True, checksize=True), name="eddy_quad")
-    get_path = lambda x: x.split('.nii.gz')[0].split('_fix')[0]
-    get_qc_path = lambda x: x.split('.nii.gz')[0] + '.qc'
-    wf.connect(prep, ('fsl_eddy.out_corrected', get_path), eddy_quad, 'base_name')
-    wf.connect(inputspec, 'bval_file', eddy_quad, 'bval_file')
-    wf.connect(prep, 'Rotate_Bvec.out_file', eddy_quad, 'bvec_file')
-    wf.connect(prep, 'peb_correction.topup.out_field', eddy_quad, 'field')
-    wf.connect(prep, 'gen_index.out_file', eddy_quad, 'idx_file')
-    wf.connect(prep, 'peb_correction.topup.out_enc_file', eddy_quad, 'param_file')
-    wf.connect(prep, ('fsl_eddy.out_corrected', get_qc_path), eddy_quad, 'output_dir')
-
-    # need a mask file for eddy_quad. lets get it from the B0.
-    def get_b0_mask_fn(b0_file):
-        import nibabel as nib
-        from nipype.utils.filemanip import fname_presuffix
-        from dipy.segment.mask import median_otsu
-        import os
-
-        mask_file = fname_presuffix(b0_file, suffix="_mask", newpath=os.path.abspath('.'))
-        img = nib.load(b0_file)
-        data, aff = img.get_data(), img.affine
-        _, mask = median_otsu(data, 2, 1)
-        nib.Nifti1Image(mask.astype(float), aff).to_filename(mask_file)
-        return mask_file
-
-
-    def id_outliers_fn(outlier_report, threshold, dwi_file):
-        """Get list of scans that exceed threshold for number of outliers
-
-        Parameters
-        ----------
-        outlier_report: string
-            Path to the fsl_eddy outlier report
-
-        threshold: int or float
-            If threshold is an int, it is treated as number of allowed outlier
-            slices. If threshold is a float between 0 and 1 (exclusive), it is
-            treated the fraction of allowed outlier slices before we drop the
-            whole volume.
-
-        dwi_file: string
-            Path to nii dwi file to determine total number of slices
-
-        Returns
-        -------
-        drop_scans: numpy.ndarray
-            List of scan indices to drop
-        """
-        import nibabel as nib
-        import numpy as np
-        import os.path as op
-        import parse
-
-        with open(op.abspath(outlier_report), 'r') as fp:
-            lines = fp.readlines()
-
-        p = parse.compile(
-            "Slice {slice:d} in scan {scan:d} is an outlier with "
-            "mean {mean_sd:f} standard deviations off, and mean "
-            "squared {mean_sq_sd:f} standard deviations off."
-        )
-
-        outliers = [p.parse(l).named for l in lines]
-        scans = {d['scan'] for d in outliers}
-
-        def num_outliers(scan, outliers):
-            return len([d for d in outliers if d['scan'] == scan])
-
-        if 0 < threshold < 1:
-            img = nib.load(dwi_file)
-            try:
-                threshold *= img.header.get_n_slices()
-            except nib.spatialimages.HeaderDataError:
-                print('WARNING. We are not sure which dimension has the '
-                      'slices in this image. So we are using the 3rd dim.', img.shape)
-                threshold *= img.shape[2]
-
-        drop_scans = np.array([
-            s for s in scans
-            if num_outliers(s, outliers) > threshold
-        ])
-
-        outpath = op.abspath("dropped_scans.txt")
-        np.savetxt(outpath, drop_scans, fmt="%d")
-
-        return drop_scans, outpath
-
-    id_outliers_node = pe.Node(niu.Function(
-        input_names=["outlier_report", "threshold", "dwi_file"],
-        output_names=["drop_scans", "outpath"],
-        function=id_outliers_fn),
-        name="id_outliers_node"
+    apply_mask_premoco_node = pe.Node(fsl.ApplyMask(), name="apply_mask_pre_moco")
+
+    # Detect and remove motion outliers
+    fsl_split_node = pe.Node(fsl.Split(dimension="t"), name="fsl_split")
+
+    pick_ref = pe.Node(niu.Select(), name="pick_ref")
+
+    coreg = pe.MapNode(
+        fsl.FLIRT(no_search=True, interp="spline", padding_size=1, dof=6),
+        name="coregistration",
+        iterfield=["in_file"],
+    )
+
+    get_motion_params_node = pe.Node(
+        niu.Function(
+            input_names=["flirt_mats"],
+            output_names=["motion_params"],
+            function=core.get_flirt_motion_parameters,
+            imports=import_list,
+        ),
+        name="get_motion_params",
+    )
+
+    fsl_merge_node = pe.Node(fsl.Merge(dimension="t"), name="fsl_merge")
+
+    art_node = pe.Node(interface=ArtifactDetect(), name="art")
+    art_node.inputs.use_differences = [True, True]
+    art_node.inputs.save_plot = False
+    art_node.inputs.use_norm = True
+    art_node.inputs.norm_threshold = 3
+    art_node.inputs.zintensity_threshold = 9
+    art_node.inputs.mask_type = "spm_global"
+    art_node.inputs.parameter_source = "FSL"
+
+    drop_outliers_fn_node = pe.Node(
+        niu.Function(
+            input_names=["in_file", "in_bval", "in_bvec", "drop_scans"],
+            output_names=["out_file", "out_bval", "out_bvec"],
+            function=core.drop_outliers_fn,
+            imports=import_list,
+        ),
+        name="drop_outliers_fn",
     )
 
-    wf.connect(inputspec, 'dwi_file', id_outliers_node, 'dwi_file')
-    wf.connect(inputspec, 'slice_outlier_threshold', id_outliers_node, 'threshold')
-
-    wf.connect(prep, "fsl_eddy.out_outlier_report",
-               id_outliers_node, "outlier_report")
-
-    list_merge = pe.Node(niu.Merge(numinputs=2), name="list_merge")
-    wf.connect(inputspec, 'dwi_file_ap', list_merge, 'in1')
-    wf.connect(inputspec, 'dwi_file_pa', list_merge, 'in2')
-
-    merge = pe.Node(fsl.Merge(dimension='t'), name="mergeAPPA")
-    wf.connect(merge, 'merged_file', prep, 'inputnode.alt_file')
-    wf.connect(list_merge, 'out', merge, 'in_files')
-
-    fslroi = pe.Node(fsl.ExtractROI(t_min=0, t_size=1), name="fslroi")
-    wf.connect(prep, "outputnode.out_file", fslroi, "in_file")
-
-    b0mask_node = pe.Node(niu.Function(input_names=['b0_file'],
-                                       output_names=['mask_file'],
-                                       function=get_b0_mask_fn),
-                          name="getB0Mask")
-    wf.connect(fslroi, 'roi_file', b0mask_node, 'b0_file')
-    wf.connect(b0mask_node, 'mask_file', eddy_quad, 'mask_file')
-
-    bbreg = pe.Node(fs.BBRegister(contrast_type="t2", init="coreg",
-                                  out_fsl_file=True,
-                                  # subjects_dir=subjects_dir,
-                                  epi_mask=True),
-                    name="bbreg")
-    bbreg.inputs.subject_id = 'freesurfer'  # bids_sub_name
-    wf.connect(fslroi, "roi_file", bbreg, "source_file")
-    wf.connect(inputspec, 'subjects_dir', bbreg, 'subjects_dir')
-
-    def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
-        """Drop outlier volumes from dwi file
-
-        Parameters
-        ----------
-        in_file: string
-            Path to nii dwi file to drop outlier volumes from
-
-        in_bval: string
-            Path to bval file to drop outlier volumes from
-
-        in_bvec: string
-            Path to bvec file to drop outlier volumes from
-
-        drop_scans: numpy.ndarray
-            List of scan indices to drop
-
-        Returns
-        -------
-        out_file: string
-            Path to "thinned" output dwi file
-
-        out_bval: string
-            Path to "thinned" output bval file
-
-        out_bvec: string
-            Path to "thinned" output bvec file
-        """
-        import nibabel as nib
-        import numpy as np
-        import os.path as op
-        from nipype.utils.filemanip import fname_presuffix
-
-        img = nib.load(op.abspath(in_file))
-        img_data = img.get_data()
-        img_data_thinned = np.delete(img_data,
-                                     drop_scans,
-                                     axis=3)
-        if isinstance(img, nib.nifti1.Nifti1Image):
-            img_thinned = nib.Nifti1Image(img_data_thinned.astype(np.float64),
-                                          img.affine,
-                                          header=img.header)
-        elif isinstance(img, nib.nifti2.Nifti2Image):
-            img_thinned = nib.Nifti2Image(img_data_thinned.astype(np.float64),
-                                          img.affine,
-                                          header=img.header)
-        else:
-            raise TypeError("in_file does not contain Nifti image datatype.")
-
-        out_file = fname_presuffix(in_file, suffix="_thinned", newpath=op.abspath('.'))
-        nib.save(img_thinned, op.abspath(out_file))
-
-        bval = np.loadtxt(in_bval)
-        bval_thinned = np.delete(bval, drop_scans, axis=0)
-        out_bval = fname_presuffix(in_bval, suffix="_thinned", newpath=op.abspath('.'))
-        np.savetxt(out_bval, bval_thinned)
-
-        bvec = np.loadtxt(in_bvec)
-        bvec_thinned = np.delete(bvec, drop_scans, axis=1)
-        out_bvec = fname_presuffix(in_bvec, suffix="_thinned", newpath=op.abspath('.'))
-        np.savetxt(out_bvec, bvec_thinned)
-
-        return out_file, out_bval, out_bvec
-
-    drop_outliers_node = pe.Node(niu.Function(
-        input_names=["in_file", "in_bval", "in_bvec", "drop_scans"],
-        output_names=["out_file", "out_bval", "out_bvec"],
-        function=drop_outliers_fn),
-        name="drop_outliers_node"
+    make_gtab_node = pe.Node(
+        niu.Function(
+            input_names=["fbval", "fbvec", "sesdir"],
+            output_names=["gtab_file", "gtab"],
+            function=core.make_gtab,
+            imports=import_list,
+        ),
+        name="make_gtab",
     )
 
-    # Align the output of drop_outliers_node & also the eddy corrected version to the anatomical space
-    # without resampling. and then for aparc+aseg & the mask, resample to the larger voxel size of the B0 image from
-    # fslroi. Also we need to apply the transformation to both bvecs (dropped & eddied) and I think we can just load
-    # the affine from bbreg (sio.loadmat) and np.dot(coord, aff) for each coord in bvec
-
-    def get_orig(subjects_dir, sub='freesurfer'):
-        import os.path as op
-        return op.join(subjects_dir, sub, "mri", "orig.mgz")
-
-    def get_aparc_aseg(subjects_dir, sub='freesurfer'):
-        import os.path as op
-        return op.join(subjects_dir, sub, "mri", "aparc+aseg.mgz")
-
-    # transform the dropped volume version to anat space w/ out resampling
-    voltransform = pe.Node(fs.ApplyVolTransform(no_resample=True),
-                           iterfield=['source_file', 'reg_file'],
-                           name='transform')
-
-    wf.connect(inputspec, 'subjects_dir', voltransform, 'subjects_dir')
-    wf.connect(inputspec, ('subjects_dir', get_aparc_aseg), voltransform, 'target_file')
-    wf.connect(prep, "outputnode.out_file", voltransform, "source_file")
-    wf.connect(bbreg, "out_reg_file", voltransform, "reg_file")
-
-    def apply_transform_to_bvecs_fn(bvec_file, reg_mat_file):
-        import numpy as np
-        import nipype.utils.filemanip as fm
-        import os
-
-        aff = np.loadtxt(reg_mat_file)
-        bvecs = np.loadtxt(bvec_file)
-        bvec_trans = []
-        for bvec in bvecs.T:
-            coord = np.hstack((bvec, [1]))
-            coord_trans = np.dot(coord, aff)[:-1]
-            bvec_trans.append(coord_trans)
-        out_bvec = fm.fname_presuffix(bvec_file, suffix="anat_space", newpath=os.path.abspath('.'))
-        np.savetxt(out_bvec, np.asarray(bvec_trans).T)
-        return out_bvec
-
-    apply_transform_to_bvecs_node = pe.Node(niu.Function(input_names=['bvec_file', 'reg_mat_file'],
-                                                         output_names=['out_bvec'],
-                                                         function=apply_transform_to_bvecs_fn),
-                                            name="applyTransformToBvecs")
-    wf.connect(bbreg, 'out_fsl_file', apply_transform_to_bvecs_node, 'reg_mat_file')
-    wf.connect(prep, 'outputnode.out_bvec', apply_transform_to_bvecs_node, 'bvec_file')
-
-    # ok cool, now lets do the thresholding.
-
-    wf.connect(id_outliers_node, "drop_scans", drop_outliers_node, "drop_scans")
-    wf.connect(voltransform, "transformed_file", drop_outliers_node, "in_file")
-    wf.connect(inputspec, 'bval_file', drop_outliers_node, 'in_bval')
-    wf.connect(apply_transform_to_bvecs_node, "out_bvec", drop_outliers_node, "in_bvec")
-
-    # lets compute the tensor on both the dropped volume scan
-    # and also the original, eddy corrected one.
-    get_tensor = pe.Node(DTI(), name="dipy_tensor")
-    wf.connect(drop_outliers_node, "out_file", get_tensor, "in_file")
-    wf.connect(drop_outliers_node, "out_bval", get_tensor, "in_bval")
-    wf.connect(drop_outliers_node, "out_bvec", get_tensor, "in_bvec")
-
-    get_tensor_eddy = get_tensor.clone('dipy_tensor_eddy')
-    wf.connect(voltransform, 'transformed_file', get_tensor_eddy, "in_file")
-    wf.connect(apply_transform_to_bvecs_node, 'out_bvec', get_tensor_eddy, "in_bvec")
-    wf.connect(inputspec, 'bval_file', get_tensor_eddy, 'in_bval')
-
-    # AK: What is this, some vestigal node from a previous workflow?
-    # I'm not sure why the tensor gets scaled. but i guess lets scale it for
-    # both the dropped & eddy corrected versions.
-    scale_tensor = pe.Node(name='scale_tensor', interface=fsl.BinaryMaths())
-    scale_tensor.inputs.operation = 'mul'
-    scale_tensor.inputs.operand_value = 1000
-    wf.connect(get_tensor, 'out_file', scale_tensor, 'in_file')
-
-    scale_tensor_eddy = scale_tensor.clone('scale_tensor_eddy')
-    wf.connect(get_tensor_eddy, 'out_file', scale_tensor_eddy, 'in_file')
-
-    # OK now that anatomical stuff (segmentation & mask)
-    # We'll need:
-    # 1. the B0 image in anat space (fslroi the 'transformed file' of voltransform
-    # 2. the aparc aseg resampled-like the B0 image (mri_convert)
-    # 3. the resample aparc_aseg binarized to be the mask image.
-
-    def binarize_aparc(aparc_aseg):
-        import nibabel as nib
-        from nipype.utils.filemanip import fname_presuffix
-        import os.path as op
-
-        img = nib.load(aparc_aseg)
-        data, aff = img.get_data(), img.affine
-        outfile = fname_presuffix(
-            aparc_aseg, suffix="bin.nii.gz",
-            newpath=op.abspath("."), use_ext=False
-        )
-        nib.Nifti1Image((data > 0).astype(float), aff).to_filename(outfile)
-        return outfile
-
-    create_mask = pe.Node(niu.Function(input_names=["aparc_aseg"],
-                                       output_names=["outfile"],
-                                       function=binarize_aparc),
-                          name="bin_aparc")
-
-    get_b0_anat = fslroi.clone('get_b0_anat')
-    wf.connect(voltransform, 'transformed_file', get_b0_anat, 'in_file')
-
-    # reslice the anat-space aparc+aseg to the DWI resolution
-    reslice_to_dwi = pe.Node(fs.MRIConvert(resample_type="nearest"),
-                             name="reslice_to_dwi")
-    wf.connect(get_b0_anat, 'roi_file', reslice_to_dwi, 'reslice_like')
-    wf.connect(inputspec, ('subjects_dir', get_aparc_aseg), reslice_to_dwi, 'in_file')
-
-    # also reslice the orig i suppose
-    reslice_orig_to_dwi = reslice_to_dwi.clone('resliceT1wToDwi')
-    wf.connect(inputspec, ('subjects_dir', get_orig), reslice_orig_to_dwi, 'in_file')
-    # reslice_orig_to_dwi.inputs.in_file = get_orig(subjects_dir, 'freesurfer')
-    reslice_orig_to_dwi.inputs.out_type = 'niigz'
-    wf.connect(get_b0_anat, 'roi_file', reslice_orig_to_dwi, 'reslice_like')
-
-    # we assume the freesurfer is the output of BIDS
-    # so the freesurfer output is in /path/to/derivatives/sub-whatever/freesurfer
-    # which means the subject_dir is /path/to/derivatives/sub-whatever
-    # reslice_to_dwi.inputs.in_file = get_aparc_aseg(subjects_dir, 'freesurfer')
-
-    # now we have a nice aparc+aseg still in anat space but resliced like the dwi file
-    # lets create a mask file from it.
-
-    wf.connect(reslice_to_dwi, 'out_file', create_mask, 'aparc_aseg')
-
-    # save all the things
-    datasink = pe.Node(nio.DataSink(), name="sinker")
-    wf.connect(inputspec, 'out_dir', datasink, 'base_directory')
-    wf.connect(inputspec, 'subject_id', datasink, 'container')
-
-    wf.connect(drop_outliers_node, "out_file", datasink, "dmriprep.dwi.@thinned")
-    wf.connect(drop_outliers_node, "out_bval", datasink, "dmriprep.dwi.@bval_thinned")
-    wf.connect(drop_outliers_node, "out_bvec", datasink, "dmriprep.dwi.@bvec_thinned")
-
-    # eddy corrected files
-    wf.connect(prep, "outputnode.out_file", datasink, "dmriprep.dwi_eddy.@corrected")
-    wf.connect(prep, "outputnode.out_bvec", datasink, "dmriprep.dwi_eddy.@rotated")
-    wf.connect(inputspec, 'bval_file', datasink, 'dmriprep.dwi_eddy.@bval')
-
-    # all the eddy stuff except the corrected files
-    wf.connect(prep, "fsl_eddy.out_movement_rms",
-               datasink, "dmriprep.qc.@eddyparamsrms")
-    wf.connect(prep, "fsl_eddy.out_outlier_report",
-               datasink, "dmriprep.qc.@eddyparamsreport")
-    wf.connect(prep, "fsl_eddy.out_restricted_movement_rms",
-               datasink, "dmriprep.qc.@eddyparamsrestrictrms")
-    wf.connect(prep, "fsl_eddy.out_shell_alignment_parameters",
-               datasink, "dmriprep.qc.@eddyparamsshellalign")
-    wf.connect(prep, "fsl_eddy.out_parameter",
-               datasink, "dmriprep.qc.@eddyparams")
-    wf.connect(prep, "fsl_eddy.out_cnr_maps",
-               datasink, "dmriprep.qc.@eddycndr")
-    wf.connect(prep, "fsl_eddy.out_residuals",
-               datasink, "dmriprep.qc.@eddyresid")
-
-    # the file that told us which volumes to drop
-    wf.connect(id_outliers_node, "outpath", datasink, "dmriprep.qc.@droppedscans")
-
-    # the tensors of the dropped volumes dwi
-    wf.connect(get_tensor, "out_file", datasink, "dmriprep.dti.@tensor")
-    wf.connect(get_tensor, "fa_file", datasink, "dmriprep.dti.@fa")
-    wf.connect(get_tensor, "md_file", datasink, "dmriprep.dti.@md")
-    wf.connect(get_tensor, "ad_file", datasink, "dmriprep.dti.@ad")
-    wf.connect(get_tensor, "rd_file", datasink, "dmriprep.dti.@rd")
-    wf.connect(get_tensor, "color_fa_file", datasink, "dmriprep.dti.@colorfa")
-    wf.connect(scale_tensor, "out_file", datasink, "dmriprep.dti.@scaled_tensor")
-
-    # the tensors of the eddied volumes dwi
-    wf.connect(get_tensor_eddy, "out_file", datasink, "dmriprep.dti_eddy.@tensor")
-    wf.connect(get_tensor_eddy, "fa_file", datasink, "dmriprep.dti_eddy.@fa")
-    wf.connect(get_tensor_eddy, "md_file", datasink, "dmriprep.dti_eddy.@md")
-    wf.connect(get_tensor_eddy, "ad_file", datasink, "dmriprep.dti_eddy.@ad")
-    wf.connect(get_tensor_eddy, "rd_file", datasink, "dmriprep.dti_eddy.@rd")
-    wf.connect(get_tensor_eddy, "color_fa_file", datasink, "dmriprep.dti_eddy.@colorfa")
-    wf.connect(scale_tensor_eddy, "out_file", datasink, "dmriprep.dti_eddy.@scaled_tensor")
-
-    # all the eddy_quad stuff
-    wf.connect(eddy_quad, 'qc_json', datasink, "dmriprep.qc.@eddyquad_json")
-    wf.connect(eddy_quad, 'qc_pdf', datasink, "dmriprep.qc.@eddyquad_pdf")
-    wf.connect(eddy_quad, 'avg_b_png', datasink, "dmriprep.qc.@eddyquad_bpng")
-    wf.connect(eddy_quad, 'avg_b0_pe_png',
-               datasink, "dmriprep.qc.@eddyquad_b0png")
-    wf.connect(eddy_quad, 'cnr_png', datasink, "dmriprep.qc.@eddyquad_cnr")
-    wf.connect(eddy_quad, 'vdm_png', datasink, "dmriprep.qc.@eddyquad_vdm")
-    wf.connect(eddy_quad, 'residuals', datasink, 'dmriprep.qc.@eddyquad_resid')
-
-    # anatomical registration stuff
-    wf.connect(bbreg, "min_cost_file", datasink, "dmriprep.reg.@mincost")
-    wf.connect(bbreg, "out_fsl_file", datasink, "dmriprep.reg.@fslfile")
-    wf.connect(bbreg, "out_reg_file", datasink, "dmriprep.reg.@reg")
-
-    # anatomical files resliced
-    wf.connect(reslice_to_dwi, 'out_file', datasink, 'dmriprep.anat.@segmentation')
-    wf.connect(create_mask, 'outfile', datasink, 'dmriprep.anat.@mask')
-    wf.connect(reslice_orig_to_dwi, 'out_file', datasink, 'dmriprep.anat.@T1w')
-
-    def report_fn(dwi_corrected_file, eddy_rms, eddy_report,
-                  color_fa_file, anat_mask_file, outlier_indices,
-                  eddy_qc_file):
-        from dmriprep.qc import create_report_json
-
-        report = create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
-                                    color_fa_file, anat_mask_file, outlier_indices,
-                                    eddy_qc_file)
-        return report
-
-    report_node = pe.Node(niu.Function(
-        input_names=['dwi_corrected_file', 'eddy_rms',
-                     'eddy_report', 'color_fa_file',
-                     'anat_mask_file', 'outlier_indices', 'eddy_qc_file'],
-        output_names=['report'],
-        function=report_fn
-    ), name="reportJSON")
-
-    # for the report, lets show the eddy corrected (full volume) image
-    wf.connect(voltransform, "transformed_file", report_node, 'dwi_corrected_file')
-    wf.connect(eddy_quad, 'qc_json', report_node, 'eddy_qc_file')
-
-    # add the rms movement output from eddy
-    wf.connect(prep, "fsl_eddy.out_movement_rms", report_node, 'eddy_rms')
-    wf.connect(prep, "fsl_eddy.out_outlier_report", report_node, 'eddy_report')
-    wf.connect(id_outliers_node, 'drop_scans', report_node, 'outlier_indices')
-
-    # the mask file to check our registration, and the colorFA file go in the report
-    wf.connect(create_mask, "outfile", report_node, 'anat_mask_file')
-    wf.connect(get_tensor, "color_fa_file", report_node, 'color_fa_file')
-
-    # save that report!
-    wf.connect(report_node, 'report', datasink, 'dmriprep.report.@report')
-
-    # this part is done last, to get the filenames *just right*
-    # its super annoying.
-    def name_files_nicely(dwi_file, subject_id):
-        import os.path as op
-
-        dwi_fname = op.split(dwi_file)[1].split(".nii.gz")[0]
-        substitutions = [
-            ("vol0000_flirt_merged.nii.gz", dwi_fname + '.nii.gz'),
-            ("stats.vol0000_flirt_merged.txt", dwi_fname + ".art.json"),
-            ("motion_parameters.par", dwi_fname + ".motion.txt"),
-            ("_rotated.bvec", ".bvec"),
-            ("art.vol0000_flirt_merged_outliers.txt", dwi_fname + ".outliers.txt"),
-            ("vol0000_flirt_merged", dwi_fname),
-            ("_roi_bbreg_freesurfer", "_register"),
-            ("dwi/eddy_corrected", "dwi/%s" % dwi_fname),
-            ("dti/eddy_corrected", "dti/%s" % dwi_fname.replace("_dwi", "")),
-            ("reg/eddy_corrected", "reg/%s" % dwi_fname.replace("_dwi", "")),
-            ("aparc+aseg_outbin", dwi_fname.replace("_dwi", "_mask")),
-            ("aparc+aseg_out", dwi_fname.replace("_dwi", "_aparc+aseg")),
-            ("art.eddy_corrected_outliers", dwi_fname.replace("dwi", "outliers")),
-            ("color_fa", "colorfa"),
-            ("orig_out", dwi_fname.replace("_dwi", "_T1w")),
-            ("stats.eddy_corrected", dwi_fname.replace("dwi", "artStats")),
-            ("eddy_corrected.eddy_parameters", dwi_fname + ".eddy_parameters"),
-            ("qc/eddy_corrected", "qc/" + dwi_fname),
-            ("derivatives/dmriprep", "derivatives/{}/dmriprep".format(subject_id)),
-            ("_rotatedanat_space_thinned", ""),
-            ("_thinned", ""),
-            ("eddy_corrected", dwi_fname),
-            ("_warped", ""),
-            ("_maths", "_scaled"),
-            ("dropped_scans", dwi_fname.replace("_dwi", "_dwi_dropped_scans")),
-            ("report.json", dwi_fname.replace("_dwi", "_dwi_report.json"))
-        ]
-        return substitutions
-
-    node_name_files_nicely = pe.Node(niu.Function(input_names=['dwi_file', 'subject_id'],
-                                                  output_names=['substitutions'],
-                                                  function=name_files_nicely),
-                                     name="name_files_nicely")
-    wf.connect(inputspec, 'dwi_file', node_name_files_nicely, 'dwi_file')
-    wf.connect(inputspec, 'subject_id', node_name_files_nicely, 'subject_id')
-    wf.connect(node_name_files_nicely, 'substitutions', datasink, 'substitutions')
+    extract_metadata_node = pe.Node(
+        niu.Function(
+            input_names=["metadata"],
+            output_names=["spec_line", "spec_acqp", "spec_slice"],
+            function=core.extract_metadata,
+            imports=import_list,
+        ),
+        name="extract_metadata",
+    )
+
+    # Gather TOPUP/EDDY inputs
+    check_shelled_node = pe.Node(
+        niu.Function(
+            input_names=["gtab_file"],
+            output_names=["check_shelled"],
+            function=core.check_shelled,
+            imports=import_list,
+        ),
+        name="check_shelled",
+    )
+
+    get_topup_inputs_node = pe.Node(
+        niu.Function(
+            input_names=["dwi", "sesdir", "spec_acqp", "b0_vols", "topup_config_odd"],
+            output_names=[
+                "datain_file",
+                "imain_output",
+                "example_b0",
+                "datain_lines",
+                "topup_config",
+            ],
+            function=core.topup_inputs_from_dwi_files,
+            imports=import_list,
+        ),
+        name="get_topup_inputs",
+    )
+
+    get_eddy_inputs_node = pe.Node(
+        niu.Function(
+            input_names=["sesdir", "gtab_file"],
+            output_names=["index_file"],
+            function=core.eddy_inputs_from_dwi_files,
+            imports=import_list,
+        ),
+        name="get_eddy_inputs",
+    )
+
+    # Run TOPUP
+    topup_node = pe.Node(fsl.TOPUP(), name="topup")
+    topup_node._mem_gb = 4
+    topup_node.n_procs = 1
+    topup_node.interface.mem_gb = 4
+    topup_node.interface.n_procs = 1
+
+    # Run BET on mean b0 of topup-corrected output
+    make_mean_b0_node = pe.Node(
+        niu.Function(
+            input_names=["in_file"],
+            output_names=["mean_file_out"],
+            function=core.make_mean_b0,
+            imports=import_list,
+        ),
+        name="make_mean_b0",
+    )
+    btr_node = pe.Node(fsl.BET(), name="bet")
+    btr_node.inputs.mask = True
+    btr_node.inputs.frac = 0.2
+
+    # Run EDDY
+    eddy_node = pe.Node(interfaces.ExtendedEddy(**eddy_args), name="eddy")
+    eddy_node.inputs.num_threads = 4
+    eddy_node._mem_gb = 8
+    eddy_node.n_procs = 4
+    eddy_node.interface.mem_gb = 8
+    eddy_node.interface.n_procs = 4
+
+    # Drop outlier volumes
+    id_outliers_fn_node = pe.Node(
+        niu.Function(
+            input_names=["outlier_report", "threshold", "dwi_file"],
+            output_names=["drop_scans", "outpath"],
+            function=core.id_outliers_fn,
+            imports=import_list,
+        ),
+        name="id_outliers_fn",
+    )
+
+    drop_outliers_fn_posteddy_node = pe.Node(
+        niu.Function(
+            input_names=["in_file", "in_bval", "in_bvec", "drop_scans"],
+            output_names=["out_file", "out_bval", "out_bvec"],
+            function=core.drop_outliers_fn,
+            imports=import_list,
+        ),
+        name="drop_outliers_fn_posteddy",
+    )
+
+    make_gtab_node_final = pe.Node(
+        niu.Function(
+            input_names=["fbval", "fbvec", "sesdir"],
+            output_names=["gtab_file", "gtab"],
+            function=core.make_gtab,
+            imports=import_list,
+        ),
+        name="make_gtab_final",
+    )
+
+    apply_mask_node = pe.Node(fsl.ApplyMask(), name="apply_mask")
+
+    # Suppress gibbs ringing and denoise
+    suppress_gibbs_node = pe.Node(
+        niu.Function(
+            input_names=["in_file", "sesdir"],
+            output_names=["gibbs_corr_data", "gibbs_free_file"],
+            function=core.suppress_gibbs,
+            imports=import_list,
+        ),
+        name="suppress_gibbs",
+    )
+    suppress_gibbs_node._mem_gb = 2
+    suppress_gibbs_node.n_procs = 1
+
+    denoise_node = pe.Node(
+        niu.Function(
+            input_names=["in_file", "sesdir", "gtab_file", "mask", "strategy"],
+            output_names=["img_data_den", "denoised_file"],
+            function=core.denoise,
+            imports=import_list,
+        ),
+        name="denoise",
+    )
+    denoise_node._mem_gb = 4
+    denoise_node.n_procs = 1
+
+    outputnode = pe.Node(
+        niu.IdentityInterface(fields=["preprocessed_data", "final_bvec", "final_bval"]),
+        name="outputnode",
+    )
+
+    wf.connect([
+                (inputnode, check_orient_and_dims_dwi_node, [("fbvec", "bvecs"),
+                                                             ("dwi", "infile"),
+                                                             ("vox_size", "vox_size"),
+                                                             ("sesdir", "outdir")]),
+                (inputnode, correct_vecs_and_make_b0s_node, [("fbval", "fbval"),
+                                                             ("sesdir", "sesdir")]),
+                (check_orient_and_dims_dwi_node, correct_vecs_and_make_b0s_node, [("bvecs", "fbvec"),
+                                                                                  ("outfile", "dwi_file")]),
+                (correct_vecs_and_make_b0s_node, btr_node_premoco, [("firstb0_file", "in_file")]),
+                (btr_node_premoco, apply_mask_premoco_node, [("mask_file", "mask_file")]),
+                (check_orient_and_dims_dwi_node, apply_mask_premoco_node, [("outfile", "in_file")]),
+                (apply_mask_premoco_node, fsl_split_node, [("out_file", "in_file")]),
+                (correct_vecs_and_make_b0s_node, pick_ref, [("firstb0", "index")]),
+                (fsl_split_node, pick_ref, [("out_files", "inlist")]),
+                (pick_ref, coreg, [("out", "reference")]),
+                (fsl_split_node, coreg, [("out_files", "in_file")]),
+                (coreg, get_motion_params_node, [("out_matrix_file", "flirt_mats")]),
+                (coreg, fsl_merge_node, [("out_file", "in_files")]),
+                (get_motion_params_node, art_node, [("motion_params", "realignment_parameters")]),
+                (fsl_merge_node, art_node, [("merged_file", "realigned_files")]),
+                (check_orient_and_dims_dwi_node, drop_outliers_fn_node, [("bvecs", "in_bvec"),
+                                                                         ("outfile", "in_file")]),
+                (inputnode, drop_outliers_fn_node, [("fbval", "in_bval")]),
+                (art_node, drop_outliers_fn_node, [("outlier_files", "drop_scans")]),
+                (inputnode, extract_metadata_node, [("metadata", "metadata")]),
+                (correct_vecs_and_make_b0s_node, check_shelled_node, [("gtab_file", "gtab_file")]),
+                (drop_outliers_fn_node, get_topup_inputs_node, [("out_file", "dwi")]),
+                (inputnode, get_topup_inputs_node, [("sesdir", "sesdir"),
+                                                    ("topup_config_odd", "topup_config_odd")]),
+                (correct_vecs_and_make_b0s_node, get_topup_inputs_node, [("b0_vols", "b0_vols")]),
+                (extract_metadata_node, get_topup_inputs_node, [("spec_acqp", "spec_acqp")]),
+                (inputnode, get_eddy_inputs_node, [("sesdir", "sesdir")]),
+                (drop_outliers_fn_node, make_gtab_node, [("out_bvec", "fbvec"),
+                                                         ("out_bval", "fbval")]),
+                (inputnode, make_gtab_node, [("sesdir", "sesdir")]),
+                (make_gtab_node, get_eddy_inputs_node, [("gtab_file", "gtab_file")]),
+                (extract_metadata_node, get_eddy_inputs_node, [("spec_acqp", "spec_acqp")]),
+                (get_topup_inputs_node, topup_node, [("datain_file", "encoding_file"),
+                                                     ("imain_output", "in_file"),
+                                                     ("topup_config", "config")]),
+                (topup_node, make_mean_b0_node, [("out_corrected", "in_file")]),
+                (make_mean_b0_node, btr_node, [("mean_file_out", "in_file")]),
+                (check_shelled_node, eddy_node, [("check_shelled", "is_shelled")]),
+                (btr_node, eddy_node, [("mask_file", "in_mask")]),
+                (get_eddy_inputs_node, eddy_node, [("index_file", "in_index")]),
+                (get_topup_inputs_node, eddy_node, [("datain_file", "in_acqp")]),
+                (topup_node, eddy_node, [("out_movpar", "in_topup_movpar"),
+                                         ("out_fieldcoef", "in_topup_fieldcoef")]),
+                (drop_outliers_fn_node, eddy_node, [("out_file", "in_file"),
+                                                    ("out_bval", "in_bval"),
+                                                    ("out_bvec", "in_bvec")]),
+                (eddy_node, id_outliers_fn_node, [("out_outlier_report", "outlier_report"),
+                                                  ("out_corrected", "dwi_file")]),
+                (inputnode, id_outliers_fn_node, [("outlier_thresh", "threshold")]),
+                (drop_outliers_fn_node, drop_outliers_fn_posteddy_node, [("out_bval", "in_bval")]),
+                (eddy_node, drop_outliers_fn_posteddy_node, [("out_corrected", "in_file"),
+                                                             ("out_rotated_bvecs", "in_bvec")]),
+                (id_outliers_fn_node, drop_outliers_fn_posteddy_node, [("drop_scans", "drop_scans")]),
+                (drop_outliers_fn_posteddy_node, apply_mask_node, [("out_file", "in_file")]),
+                (btr_node, apply_mask_node, [("mask_file", "mask_file")]),
+                (apply_mask_node, suppress_gibbs_node, [("out_file", "in_file")]),
+                (inputnode, denoise_node, [("strategy", "strategy")]),
+                (btr_node, denoise_node, [("mask_file", "mask")]),
+                (drop_outliers_fn_posteddy_node, make_gtab_node_final, [("out_bvec", "fbvec"),
+                                                                        ("out_bval", "fbval")]),
+                (inputnode, make_gtab_node_final, [("sesdir", "sesdir")]),
+                (make_gtab_node_final, denoise_node, [("gtab_file", "gtab_file")]),
+                (suppress_gibbs_node, denoise_node, [("gibbs_free_file", "in_file")]),
+                (inputnode, suppress_gibbs_node, [("sesdir", "sesdir")]),
+                (inputnode, denoise_node, [("sesdir", "sesdir")]),
+                (denoise_node, outputnode, [("denoised_file", "preprocessed_data")]),
+                (drop_outliers_fn_posteddy_node, outputnode, [("out_bvec", "final_bvec"),
+                                                              ("out_bval", "final_bval")])
+                ])
+
+    if verbose is True:
+        from nipype import config, logging
+        cfg_v = dict(logging={'workflow_level': 'DEBUG', 'utils_level': 'DEBUG', 'interface_level': 'DEBUG',
+                              'log_directory': str(wf.base_dir), 'log_to_file': True},
+                     monitoring={'enabled': True, 'sample_frequency': '0.1', 'summary_append': True,
+                                 'summary_file': str(wf.base_dir)})
+        logging.update_logging(config)
+        config.update_config(cfg_v)
+        config.enable_debug_mode()
+        config.enable_resource_monitor()
+
+        import logging
+        callback_log_path = "%s%s" % (wf.base_dir, '/run_stats.log')
+        logger = logging.getLogger('callback')
+        logger.setLevel(logging.DEBUG)
+        handler = logging.FileHandler(callback_log_path)
+        logger.addHandler(handler)
+
+    # Set runtime/logging configurations
+    cfg = dict(
+        execution={
+            "stop_on_first_crash": True,
+            "hash_method": "content",
+            "crashfile_format": "txt",
+            "display_variable": ":0",
+            "job_finished_timeout": 65,
+            "matplotlib_backend": "Agg",
+            "plugin": str(plugin_type),
+            "use_relative_paths": True,
+            "parameterize_dirs": True,
+            "remove_unnecessary_outputs": False,
+            "remove_node_directories": False,
+            "raise_insufficient": True,
+            "poll_sleep_duration": 0.01,
+        }
+    )
+    for key in cfg.keys():
+        for setting, value in cfg[key].items():
+            wf.config[key][setting] = value
+
+    try:
+        wf.write_graph(graph2use="colored", format='png')
+    except:
+        pass
 
     return wf
diff --git a/dmriprep/utils.py b/dmriprep/utils.py
index cd92cc1..7e90d39 100644
--- a/dmriprep/utils.py
+++ b/dmriprep/utils.py
@@ -2,10 +2,8 @@
 Utility functions for other submodules
 
 """
-import itertools
-
 import numpy as np
-
+from nipype import logging
 
 mod_logger = logging.getLogger(__name__)
 
@@ -33,6 +31,8 @@ def is_hemispherical(vecs):
     ----------
     https://rstudio-pubs-static.s3.amazonaws.com/27121_a22e51b47c544980bad594d5e0bb2d04.html  # noqa
     """
+    import itertools
+
     if vecs.shape[1] != 3:
         raise ValueError("Input vectors must be 3D vectors")
     if not np.allclose(1, np.linalg.norm(vecs, axis=1)):
@@ -64,3 +64,14 @@ def is_hemispherical(vecs):
     else:
         pole = np.array([0.0, 0.0, 0.0])
     return is_hemi, pole
+
+
+def merge_dicts(x, y):
+    """
+    A function to merge two dictionaries, making it easier for us to make
+    modality specific queries for dwi images (since they have variable
+    extensions due to having an nii.gz, bval, and bvec file).
+    """
+    z = x.copy()
+    z.update(y)
+    return z
diff --git a/requirements.txt b/requirements.txt
index b780e72..e6e47c6 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,11 +1,11 @@
 Click>=6.0
-dask==1.2.2
-dipy==0.16.0
-nipype==1.2.0
-pandas==0.24.2
-parse==1.12.0
-tqdm==4.32.1
-pybids==0.8.0
-matplotlib==3.1.0
-cytoolz==0.9.0.1
-numba==0.43.1
\ No newline at end of file
+dask>=1.2.2
+dipy>=1.0.0
+nipype>=1.2.0
+pandas>=0.24.2
+parse>=1.12.0
+tqdm>=4.32.1
+pybids>=0.8.0
+matplotlib>=3.1.0
+cytoolz>=0.9.0.1
+numba>=0.43.1