min PLD update

.gitignore

@@ -14,3 +14,7 @@ full_analysis.prj
 build_and_deploy.sh
 app_old/for_testing/full_analysis
 bfg-1.13.1.jar
+app/old/
+full_analysis07
+app/full_analysis07/for_redistribution_files_only/full_analysis
+app/full_analysis07.zip

Dockerfile

@@ -89,10 +89,10 @@ ENV FLYWHEEL /flywheel/v0
 RUN mkdir -p ${FLYWHEEL}
 RUN mkdir -p ${FLYWHEEL}/opt
 
-# Install MCR. Install path: usr/local/MATLAB/MATLAB_Runtime/v97
-RUN wget -O opt/mcr.zip http://ssd.mathworks.com/supportfiles/downloads/R2019b/Release/0/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2019b_glnxa64.zip
-RUN unzip opt/mcr.zip -d opt/
-RUN opt/install -mode silent -agreeToLicense yes
+# Install MCR. Install path: /usr/local/MATLAB/MATLAB_Runtime/v97
+RUN wget -O /opt/mcr.zip http://ssd.mathworks.com/supportfiles/downloads/R2019b/Release/0/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2019b_glnxa64.zip
+RUN unzip /opt/mcr.zip -d /opt/
+RUN /opt/install -mode silent -agreeToLicense yes
 
 # Install libs
 RUN apt-get -y install libxmu6
@@ -102,7 +102,9 @@ COPY . /flywheel/v0/
 RUN chmod +x ${FLYWHEEL}/*
 
 # Change permissions
-RUN chmod 777 /
+#RUN chmod 777 /
+RUN chmod 777 ${FLYWHEEL}/app/full_analysis07/for_redistribution_files_only/run_full_analysis.sh
+RUN chmod 777 ${FLYWHEEL}/app/full_analysis07/for_redistribution_files_only/full_analysis
 
 # ENV preservation for Flywheel Engine
 RUN env -u HOSTNAME -u PWD | \

manifest.json

@@ -2,7 +2,7 @@
 	"name": "hasl-decode",
 	"label": "HASL Decoder: Hadamard-encoded ASL (HASL) processing pipeline",
 	"description": "Hadamard-encoded multi-delay ASL data(HASL) processing pipeline for measuring cerebrovascular reactivity. Decodes the Hadamard matrix into three post-labelling delays and calculates cerebral blood flow, arterial transit time and transit time-corrected cerebral blood flow.",
-	"version": "0.6.2_0.6.2",
+	"version": "0.7.3_0.8.1",
 	"inputs": {
 		"asl": {
 			"base": "file",
@@ -41,7 +41,7 @@
 	"custom": {
 		"gear-builder": {
 			"category": "analysis",
-			"image": "willtack/hasl:0.6.2"
+			"image": "willtack/hasl:0.7.3_0.8.1"
 		},
 		"flywheel": {
 			"suite": "BrainScienceCenter"

run

@@ -22,7 +22,7 @@ FLYWHEEL_BASE=/flywheel/v0
 MCR_ROOT=/usr/local/MATLAB/MATLAB_Runtime/v97/  # double check this
 INPUT_DIR=${FLYWHEEL_BASE}/input
 OUTPUT_DIR=${FLYWHEEL_BASE}/output
-CODE_DIR=${FLYWHEEL_BASE}/app/full_analysis/07/for_redistribution_files_only
+CODE_DIR=${FLYWHEEL_BASE}/app/full_analysis07/for_redistribution_files_only
 
 # Make sure that /output directory exists
 if [[ ! -d "${OUTPUT_DIR}" ]]
@@ -54,6 +54,8 @@ bet2 "${mprageFile}" "${mprageFileBet}" -v -f 0.5 -g 0
 
 
 # Run the Matlab executable
+chmod +x ${CODE_DIR}/run_full_analysis.sh
+chmod +x ${CODE_DIR}/full_analysis
 time ${CODE_DIR}/run_full_analysis.sh "${MCR_ROOT}"\
                                       "${aslFile}"\
                                       "${m0File}"\

src/full_analysis.m

@@ -119,7 +119,7 @@
 asl_para = auxil_asl_para_init();
 
 asl_para.LD = 3.5;
-asl_para.PLD = 0.7;
+asl_para.PLD = 1.0;
 asl_para.PLD_Num = 7;
 asl_para.PLD_Lin = 0.5;
 asl_para.T1b = 1.65;
@@ -171,7 +171,24 @@
 
 nii.hdr.dime.dim(5)=1;
 nii.img = ttccbf_img(:,:,:,4);
-save_nii(nii, fullfile(subj_folder, 'ttcbf.nii'));
+save_nii(nii, fullfile(subj_folder, 'ttcbf4.nii'));
+
+nii.hdr.dime.dim(5)=1;
+nii.img = ttccbf_img(:,:,:,1);
+save_nii(nii, fullfile(subj_folder, 'ttcbf1.nii'));
+
+nii.hdr.dime.dim(5)=1;
+nii.img = ttccbf_img(:,:,:,6);
+save_nii(nii, fullfile(subj_folder, 'ttcbf6.nii'));
+
+nii.hdr.dime.dim(5)=1;
+nii.img = ttccbf_img(:,:,:,7);
+save_nii(nii, fullfile(subj_folder, 'ttcbf7.nii'));
+
+nii.hdr.dime.dim(5)=1;
+nii.img = ttccbf_img(:,:,:,7);
+save_nii(nii, fullfile(subj_folder, 'ttcbf8.nii'));
+
 
 tt_img = tt_img.*1000; % *1000:change unit from 's' to 'ms'
 nii.hdr.dime.dim(5)=1;