An Introduction to the Java Image Science Toolkit

Transcription

1 An Introduction to the Java Image Science Toolkit

2 JIST: A History What is JIST? Installation MIPAV JIST JIST and MIPAV Introduction to MIPAV Functionality JIST Tools Basic JIST Pipelines DTI Pipeline 2

3 To install MIPAV and JIST successfully Understand the basic pieces of JIST Have an idea of how to build large pipelines 3

4 Java Image Science Toolkit Plugin for MIPAV or standalone application Tool for voxel level analysis of imaging data Rapid framework and prototyping environment for image processing algorithms 4

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8 Select Release Version If using Windows or Linux, select 32- or 64- bit version depending on your OS (though 64- bit is preferred). 8

9 Run the basic installer 9

10 Increase the amount of ram to at least 1024 MB Ideally 8000 MB for larger analyses 10

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12 Tools and Algorithms Slices Components 12

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14 Visit Useful Links for JIST 14

15 Click on Download Now 15

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17 Select Install Plugin Restart MIPAV 17

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20 JIST and related plugins now found 20

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23 1. Scroll down to Volumes 2. Open the folder 3. Drag Volume Collection into the Layout Tool December 17, 2009 Kirby Center Thursday Morning 23

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25 Add the Random Volume Generator 1. Search in the Plugin Selector for Random Volume 1. Press Filter 2. Drag plugin into Layout Do the same for the Adding Noise Plugin 25

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27 1. Select the Random Volume Generator Module 2. Set dimensions to x:170, y:256, z:256 (dimensions of input image) 3. Set Maximum Value to 500,000 27

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30 Modifying the layout settings 1. Select Project - > Layout Preferences 30

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34 1. Select Scheduler - > Start Schedule 1. The pipeline will then run the random noise module then the summation module 34

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38 1. Right Click on Adding Noise Module 2. Select Experiments - > exp AA - > Volume Rendering - > Output Volumes - > Image Volume Corrupted with Noise 38

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40 1. Loaded data in with the Volume Collection Plugin. 2. Added Random Noise with Random Volume Generator and Adding Noise Functions. 3. Used Process Manager to run the job. 4. Modified Random Noise parameters to fit the input image. 5. Visualized the output image 40

41 Pre- built layout and dataset for DTI available at Layout recently updated to JIST 3.0 File - > Open DTI_layout.layoutXML 41

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43 To Run DTI Layout 1. Change the file location for Volume File List to where KKI DTI.nii.gz was saved 2. Change the file location for File Collection to where KKI DTI.par was saved 3. Change the file location for T2 to where KKI T2w.nii.gz was saved 43

44 To Run DTI Layout 1. Select VABRA (large, wide module) 2. Change to file:/<path>/<to>/mipav/plugins/edu/ jhu/ece/iacl/algorithms/vabra/config.xml 44

45 To Run DTI Layout 1. Change to output directory in Project - > Layout Preferences to somewhere on your machine 45

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48 How to Determine how Many Processes to run 1. Determine how many processors/threads your computer can run at a given time 1. Many CPUs this is the number of cores your computer has i.e. dual- core is two quad- core is four 2. Some Intel CPUs can run Hyper- threading which allows two threads to be run simultaneously on one processing unit 1. Google your Intel processor to determine this info 2. Hyper- threading may need to be enabled 48

49 How to Determine how Many Processes to run 1. Determine how many processors/threads your computer can run at a given time 2. Decide how much you want your computer to do simultaneously 1. Do you plan on using your computer for anything while you are running JIST? 49

50 How to Determine how Many Processes to run 1. Determine how many processors/threads your computer can run at a given time 2. Decide how much you want your computer to do simultaneously 3. Decide how many processors to use based on whats available and what you plan on doing 50

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52 To Run DTI Layout 1. Open the Process Manager (Project - > Process Manager) and select Schedule - > Start Scheduler 52

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54 Debugging the error 1. Click on the module in the Process Manager 2. Right- Click and select View Debugging Information 54

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56 Debugging the error 1. First few lines should contain error information 1. Parameters were possibly incorrect, insufficient, etc. 2. If you can t figure it out, post to the forum 1. Be sure to include stdout and stderr from debugging 2. Layout file (ideally minimum layout that causes the error) 3. Example files 56

57 After ~3 hours of running on 6 cores Colormap output 57

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61 Pre- built layout and dataset for Camino Tensor Estimation (JIST- Restore) available at Layout currently being updated to JIST 3.0 File - > Open CATNAP- RESTORE- 2009Oct10.layout (will be updated soon) 61

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63 Update parameters according to jist:restore#example 63

64 Run the process manager 64

65 Outputs of various modules should be 65

66 Running JIST on ACCRE Building JIST Modules Other JIST modules of interest 66

67 JIST I Paper JIST II Paper Next_Generation_of_JIST.pdf JIST Installation Tutorial JIST First Time Tutorial JIST FAQ QAO JIST DTI JIST with CAMINO 67

68 Questions? 68