From d681da214b286a787331c243387aa6052ff2c082 Mon Sep 17 00:00:00 2001
From: "Timothy B. Brown" <tbbrown@wustl.edu>
Date: Mon, 24 Apr 2017 11:17:35 -0500
Subject: [PATCH] Fixed problem with low res mesh option in
 ReApplyFixPipeline.sh - restored it to being an optional parameter.

---
 .../DeDriftAndResamplePipeline.sh               |  4 ++--
 ReApplyFix/ReApplyFixPipeline.sh                | 17 +++++++++--------
 version.txt                                     |  2 +-
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/DeDriftAndResample/DeDriftAndResamplePipeline.sh b/DeDriftAndResample/DeDriftAndResamplePipeline.sh
index 44c74379a..e095df6b0 100755
--- a/DeDriftAndResample/DeDriftAndResamplePipeline.sh
+++ b/DeDriftAndResample/DeDriftAndResamplePipeline.sh
@@ -158,7 +158,7 @@ get_options()
 				index=$(( index + 1 ))
 				;;
 			--smoothing-fwhm=*)
-				g_SmoothingFWHM=${argument#*=}
+				p_SmoothingFWHM=${argument#*=}
 				index=$(( index + 1 ))
 				;;
 			--highpass=*)
@@ -198,7 +198,7 @@ get_options()
 		log_Err "Subject ID (--subject=) required"
 		error_count=$(( error_count + 1 ))
 	else
-		log_Msg "Subject: ${p_subject}"
+		log_Msg "Subject: ${p_Subject}"
 	fi
 
 	if [ -z "${p_HighResMesh}" ]; then
diff --git a/ReApplyFix/ReApplyFixPipeline.sh b/ReApplyFix/ReApplyFixPipeline.sh
index 7a4105424..49ef7dc5e 100755
--- a/ReApplyFix/ReApplyFixPipeline.sh
+++ b/ReApplyFix/ReApplyFixPipeline.sh
@@ -51,7 +51,7 @@ PARAMETERs are [ ] = optional; < > = user supplied value
    --fmri-name=TBW
    --high-pass=TBW
    --reg-name=TBW
-   --low-res-mesh=TBW
+  [--low-res-mesh=TBW]
   [--matlab-run-mode={0, 1}] defaults to ${G_DEFAULT_MATLAB_RUN_MODE}
      0 = Use compiled MATLAB
      1 = Use interpreted MATLAB
@@ -77,6 +77,7 @@ get_options()
 	unset p_MatlabRunMode
 
 	# set default values
+	p_LowResMesh=${G_DEFAULT_LOW_RES_MESH}
 	p_MatlabRunMode=${G_DEFAULT_MATLAB_RUN_MODE}
 
 	# parse arguments
@@ -169,13 +170,10 @@ get_options()
 		log_Msg "Reg Name: ${p_RegName}"
 	fi
 
-	if [ -z "${p_LowResMesh}" ]; then
-		log_Err "Low Res Mesh: (--low-res-mesh=) required"
-		error_count=$(( error_count + 1 ))
-	else
+	if [ ! -z "${p_LowResMesh}" ]; then
 		log_Msg "Low Res Mesh: ${p_LowResMesh}"
 	fi
-
+	
 	if [ -z "${p_MatlabRunMode}" ]; then
 		log_Err "MATLAB run mode value (--matlab-run-mode=) required"
 		error_count=$(( error_count + 1 ))
@@ -280,8 +278,8 @@ main()
 	else
 		RegString=""
 	fi
-
-	if [ ! -z ${LowResMesh} ] && [ ${LowResMesh} != "32" ]; then
+	
+	if [ ! -z ${LowResMesh} ] && [ ${LowResMesh} != ${G_DEFAULT_LOW_RES_MESH} ]; then
 		RegString="${RegString}.${LowResMesh}k"
 	fi
 
@@ -422,6 +420,9 @@ show_tool_versions
 # Establish default MATLAB run mode
 G_DEFAULT_MATLAB_RUN_MODE=1		# Use interpreted MATLAB
 
+# Establish default low res mesh
+G_DEFAULT_LOW_RES_MESH=32
+
 # Determine whether named or positional parameters are used
 if [[ ${1} == --* ]]; then
 	# Named parameters (e.g. --parameter-name=parameter-value) are used
diff --git a/version.txt b/version.txt
index a2e813f3b..5db50a031 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-Development after: v3.22.0-beta.5 - MATLAB version and other updates
+Development: Update DeDriftAndResample pipeline for release 4.0.0