Aneurysm

Aneurysm is a collection of Java plugins for ImageJ http://imagej.nih.gov/ij/ extracting arteries from MRI images, finding centerlines and measuring tortuosity or twsitedness. The software was developed to measure the connection between tortuosity and the development of intracranial aneurysms at the University of Utah.

References

If using this software or deriving works please reference one of the following:

• Diedrich KT, Roberts JA, Schmidt RH, Parker DL. Comparing Performance of Centerline Algorithms for Quantitative Assessment of Brain Vascular Anatomy. Anat Rec (Hoboken). 2012; doi:10.1002/ar.22603
  • http://www.ncbi.nlm.nih.gov/pubmed/23060363
• Diedrich KT, Roberts JA, Schmidt RH, Albright LAC, Yetman AT, Parker DL. Medical record and imaging evaluation to identify arterial tortuosity phenotype in populations at risk for intracranial aneurysms. AMIA Annu Symp Proc. 2011;2011: 295–304.
• http://www.ncbi.nlm.nih.gov/pubmed/22195081
• Diedrich KT, Roberts JA, Schmidt RH, Kang C-K, Cho Z-H, Parker DL. Validation of an arterial tortuosity measure with application to hypertension collection of clinical hypertensive patients. BMC Bioinformatics. 2011;12 Suppl 10: S15. doi:10.1186/1471-2105-12-S10-S15
  • http://www.ncbi.nlm.nih.gov/pubmed/22166145

Additional references using this Aneurysm software

• Wei F, Diedrich KT, Fullerton HJ, deVeber G, Wintermark M, Hodge J, et al. Arterial Tortuosity: An Imaging Biomarker of Childhood Stroke Pathogenesis? Stroke. 2016; doi:10.1161/STROKEAHA.115.011331
  • http://www.ncbi.nlm.nih.gov/pubmed/27006453

ImageJ plugin

Place the Aneurysm source in ImageJ/plugins/Aneurym

ImageJ needs access to the java interpreter. Use the interpreter withe the JDK if developing. http://www.oracle.com/technetwork/java/javase/downloads/index.html On windows \ImageJ\ImageJ.cfg Has something like . C:\Program Files\Java\jdk\bin\javaw.exe -Xmx6000m -cp C:\PROGRA~1\Java\jdk\lib\tools.jar;ij.jar ij.ImageJ

On Linux image is started with imagej -c

Jar files

ImageJ needs to access Jars. They can be placed in the Java lib/ext directory Apache commons CLI for reading command line options https://commons.apache.org/proper/commons-cli/ MySQL/MariaDB connector https://downloads.mariadb.org/connector-java/

Path to Java \Java\jdk\jre\lib\ext commons-cli-1.2.jar mysql-connector-java-5.1.18-bin.jar ij.jar

ij.jar is from the ImageJ installation

Database

An optional database stores stores measurements in MySQL or MariaDB 5.5 https://mariadb.org/ -- initializing users -- mysql -u root -p -- create database aneurysm; -- create user 'userone'@'%' identified by 'password'; -- grant all on . to 'userone'@'%';

-- connecting to database -- mysql -u userone -D aneurysm -p

-- reloading backup that will generate all tables -- mysql -u userone -D aneurysm -p < sql/aneurysmdump.sql -- sql/delete_data.sql will clean the database for a fresh start

Compile

Compile the source code with Ant http://ant.apache.org/bindownload.cgi The default ant task will build the sources into the directory in build.properties ../Aneurysm-build/Aneurysm $ ant Adjust build.properties to build into a different directory

For ImageJ and Java to find the data files fill out and put config/aneurysm.properties in the $Home directory

R for analysis

R is used for visualing the data with functions in Aneurysm/R/aneurysm.R R needs the extra packages install.packages(MASS) ; install.packages( RMySQL); install.packages(RODBC); install.packages(rgl);

for connecting R to mysql rename and add configuration to config/my.cnf and place in ~/.my.cnf on Linux/UNIX/Mac OS X place in C:\my.cnf for Windows

Notes on using ODBC and R because RMySQL is not running on 64 bit windows yet

Packages
Connector/ODBC 5.1.4 http://dev.mysql.com/downloads/connector/odbc/5.1.html Control Panel -> Adminstrator tools -> Add ODBC data sources -> MySQL data source install.packages(RODBC) aneurysm is ODBC source ocon<- odbcConnect("aneurysm", uid="userone", pwd="*******") res <- sqlQuery(ocon, "select * from aneurysm") str(res)

/*========================================================================= *

• Copyright (c) Karl T. Diedrich
• Licensed under the Apache License, Version 2.0 (the "License");
• you may not use this file except in compliance with the License.
• You may obtain a copy of the License at

•     http://www.apache.org/licenses/LICENSE-2.0.txt
  

• Unless required by applicable law or agreed to in writing, software
• distributed under the License is distributed on an "AS IS" BASIS,
• WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
• See the License for the specific language governing permissions and
• limitations under the License.

=========================================================================/