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==Scanco Finite Element Analysis==


===Running the FE code on the VMS system===
Read the PDF file that is located in the "documents" directory for documentation and pick a problem number and output type. Make sure that your image is suitable for the slected analysis (see page 7 in the Scanco FE guide). You can use your segmented AIM from morphological analysis for FE analysis.
Edit the IPl file used in batch job mode <code>DISK1:[MICROCT.EVAL]IPL_FE_VM.COM</code> on percy to include the desired analysis, e.g.:
<pre>
FE_PROBLEM :== 9 !combination of 1 - 6
FE_PAR_NO :== 42 ! von Mises equivalent stress
</pre>
Start the evaluation as a batch job in queue SC3309_FE
<pre>$ fem DISK3:[MICROCT.PROJECTS.DEFROM.MODELS]SHAM_A12_W12_SEG.AIM</pre>
Look at the log file <code>SYS$SCRATCH:SHAM_A12_W12_SEG_FE.LOG</code> during execution to  verify the process.
The job is submitted using:
<pre>
SUBMIT/NOPRINT/NOTIF/LOG=SYS$SCRATCH:SHAM_A12_W12_SEG_FE.LOG/QUE=UCT_FE_QUEUE UE:IPL_FE_VM.COM/PARA=DISK3:[MICROCT.PROJECTS.DEFROM.MODELS]SHAM_A12_W12_SEG.AIM
</pre>
You can copy the <code>IPL_FE_VM.COM</code> to your project directory and use the above command to submit it.
Alternatively, FE analysis can be run interactively
<pre>$ iplfe</pre>
===Extracting results===
Creates a total result file called <code>.post</code> file. 
Then, by default, it extracts one parameter (e.g. von mises stress), and produces stats file
<code>.postlist</code> and a colorful <code>.aim</code> file (<code>_fe_par_42.aim</code>)
which you can view with uct_3d.
If you then want other parameters extracted, or other colorful images, you only
need to do a very quick operation in iplfe:
<pre>
$ iplfe
/fe_post
</pre>
give .post file and write out the resulting .aim file, and it produces also the .postlist file.


==Scanco Image Registration==
==Scanco Image Registration==

Revision as of 15:45, 16 September 2010








Scanco Image Registration

On percy, check out the DISK1:[MICROCT.EVAL]IPL_REGISTER*.COM scripts. You can also use it interactively by starting 

$ iplreg
ipl> register
ipl> transform

Use the ipl help function for more info and read the PDF guide (in Documents).

SimilarityRegistration

Understanding rotation parameters (versors)

In SimilarityRegistration, former AppSimilarityRegistrationV3, used when registering images with Shape, the config file allows for setting inital rotations initial_transform_axis_x, initial_transform_axis_y, initial_transform_axis_z. These correspond to the versor components and are calculated as follows: 

initial_transform_axis_x = n_x * sin(alpha/2)
initial_transform_axis_y = n_y * sin(alpha/2)
initial_transform_axis_z = n_z * sin(alpha/2)

where n=[n_x,n_y,n_z]^T is the unit vecotr representing the axis of rotation and alpha is the angle of rotation. Example 45 degree rotation around x-axis: 

initial_transform_axis_x = 1 * sin(45/2) = 0.382
initial_transform_axis_y = 0 * sin(45/2) = 0
initial_transform_axis_z = 0 * sin(45/2) = 0

The rotations after registration final_transform_axis_x, final_transform_axis_y, final_transform_axis_z can be interpreted the same way. ITK provides the functions GetAxis() and GetAngle to obtain [n_x, n_y, n_z] and alpha respectively, which are calculated as follows: 

v_1 = initial_transform_axis_x
v_2 = initial_transform_axis_y
v_3 = initial_transform_axis_z
magnitude = sqrt(v_1^2 + v_2^2 + v_3^2)
n_x = v_1/magnitude
n_y = v_2/magnitude
n_z = v_3/magnitude
alpha = 2 * atan(magnitude/1)

Statistics and Analysis

JAGS (analysis of Bayesian models using Markov Chain Monte Carlo)

See JAGS Usage.

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