update

Author: Antonios Makropoulos

CHANGES.txt

@@ -0,0 +1,7 @@
+The following changes have been made in the dHCP Structural Pipeline v1.1 compared to v1.0:
+- T1 is registered to T2 with an initial rigid registration, and a consequent BBR registration
+- Myelin mapping (T1/T2 ratio) is calculated prior to bias field correction
+- Cortical thickness is estimated the average distance between a) the Euclidean distance from the
+    white surface to the closest vertex in the pial surface and b) the Euclidean distance from the pial
+    surface to the closest vertex in the white surface
+- Fast collision detection is disabled in white and pial surface reconstruction

README.md

@@ -1,4 +1,4 @@
-# dHCP Structural Pipeline
+# dHCP Structural Pipeline v1.1
 
 ![pipeline image](structural_pipeline.png)
 
@@ -130,7 +130,7 @@ The setup script installs the following software packages.
 | <a href="https://github.com/Kitware/VTK">VTK</a>      | 7.0.0     
 | <a href="https://github.com/Washington-University/workbench">Connectome Workbench</a>  | 1.2.2  
 | <a href="https://github.com/BioMedIA/MIRTK">MIRTK</a>  | dhcp-v1
-| <a href="https://github.com/rob-wright/SphericalMesh">SphericalMesh</a>  | dhcp-v1
+| <a href="https://github.com/amakropoulos/SphericalMesh">SphericalMesh</a>  | dhcp-v1.1
 
 The '-h' argument can be specified to provide more setup options:
 * ./setup.sh -h
@@ -161,5 +161,9 @@ Examples:
 * ./dhcp-pipeline.sh subject2 session1 36 -T2 subject2-T2.nii.gz -T1 subject2-T1.nii.gz 
 * ./dhcp-pipeline.sh subject3 session4 28 -T2 subject3-T2.nii.gz 
 
-If the user would like to execute a specific script of the pipeline (e.g. scripts/segmentation/pipeline.sh ), the following command needs to be run first in order to setup the environment:
-* . parameters/configuration.sh
+The output of the pipeline is the following directories:
+* sourcedata   : folder containing the source images (T1,T2) of the processed subjects
+* derivatives  : folder containing the output of the pipeline processing
+
+Measurements and reporting for the dHCP Structural Pipeline can be additionally computed using this <a href="https://github.com/amakropoulos/structural-pipeline-measures">package</a>.
+

scripts/misc/pipeline.sh

@@ -54,7 +54,7 @@ threads=1
 
 # check whether the different tools are set and load parameters
 codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-. $codedir/parameters/configuration.sh
+. $codedir/../../parameters/configuration.sh
 
 shift; shift
 while [ $# -gt 0 ]; do

scripts/segmentation/pipeline.sh

@@ -31,7 +31,7 @@ threads=1
 
 # check whether the different tools are set and load parameters
 codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-. $codedir/parameters/configuration.sh
+. $codedir/../../parameters/configuration.sh
 
 shift; shift; shift
 while [ $# -gt 0 ]; do

scripts/surface/pipeline.sh

@@ -41,7 +41,7 @@ threads=1
 
 # check whether the different tools are set and load parameters
 codedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-. $codedir/parameters/configuration.sh
+. $codedir/../../parameters/configuration.sh
 
 shift
 while [ $# -gt 0 ]; do

setup.sh

@@ -200,9 +200,9 @@ set_if_undef MIRTK_build="$pipeline_build/MIRTK/build"
 set_if_undef MIRTK_cmake_flags="-DMODULE_Deformable=ON -DMODULE_DrawEM=ON -DDEPENDS_Eigen3_DIR=$code_dir/ThirdParty/eigen-eigen-67e894c6cd8f -DWITH_VTK=ON -DDEPENDS_VTK_DIR=$VTK_build -DWITH_TBB=ON"
 
 set_if_undef SPHERICALMESH_install=1
-set_if_undef SPHERICALMESH_git=https://github.com/rob-wright/SphericalMesh.git
-set_if_undef SPHERICALMESH_branch=dhcp
-set_if_undef SPHERICALMESH_version=9b73f43d85206ee7f15aee9b17f7fe07813bca14
+set_if_undef SPHERICALMESH_git=https://github.com/amakropoulos/SphericalMesh.git
+set_if_undef SPHERICALMESH_branch=dhcp-v1.1
+set_if_undef SPHERICALMESH_version=c41824cda791b806f79b88f2b27604a2f3268d19
 set_if_undef SPHERICALMESH_folder="$pipeline_build/SphericalMesh"
 set_if_undef SPHERICALMESH_build="$pipeline_build/SphericalMesh/build"
 set_if_undef SPHERICALMESH_cmake_flags="-DMIRTK_DIR=$MIRTK_build/lib/cmake/mirtk -DVTK_DIR=$VTK_build"