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| __TOC__
| | #REDIRECT [[Main Page]] |
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| ==Scanco Finite Element Analysis==
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| ===Running the FE code on the VMS system===
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| 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.
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| 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.:
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| <pre>
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| FE_PROBLEM :== 9 !combination of 1 - 6
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| FE_PAR_NO :== 42 ! von Mises equivalent stress
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| </pre>
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| Start the evaluation as a batch job in queue SC3309_FE
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| <pre>$ fem DISK3:[MICROCT.PROJECTS.DEFROM.MODELS]SHAM_A12_W12_SEG.AIM</pre>
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| Look at the log file <code>SYS$SCRATCH:SHAM_A12_W12_SEG_FE.LOG</code> during execution to verify the process.
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| The job is submitted using:
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| <pre>
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| SUBMIT/NOPRINT/NOTIF/LOG=SYS$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
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| </pre>
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| You can copy the <code>IPL_FE_VM.COM</code> to your project directory and use the above command to submit it.
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| Alternatively, FE analysis can be run interactively
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| <pre>$ iplfe</pre>
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| ===Extracting results===
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| Creates a total result file called <code>.post</code> file.
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| Then, by default, it extracts one parameter (e.g. von mises stress), and produces stats file
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| <code>.postlist</code> and a colorful <code>.aim</code> file (<code>_fe_par_42.aim</code>)
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| which you can view with uct_3d.
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| If you then want other parameters extracted, or other colorful images, you only
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| need to do a very quick operation in iplfe:
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| <pre>
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| $ iplfe
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| /fe_post
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| </pre>
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| give .post file and write out the resulting .aim file, and it produces also the .postlist file.
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| ==Scanco Image Registration==
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| On percy, check out the <code>DISK1:[MICROCT.EVAL]IPL_REGISTER*.COM</code> scripts.
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| You can also use it interactively by starting
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| <pre>
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| $ iplreg
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| ipl> register
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| ipl> transform
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| </pre>
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| Use the ipl help function for more info and read the PDF guide (in Documents).
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| ==SimilarityRegistration==
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| ===Understanding rotation parameters (versors)===
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| In SimilarityRegistration, former AppSimilarityRegistrationV3, used when registering images with Shape, the config file
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| allows for setting inital rotations <code>initial_transform_axis_x, initial_transform_axis_y, initial_transform_axis_z</code>. These correspond to the versor components and are calculated as follows:
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| <pre>
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| initial_transform_axis_x = n_x * sin(alpha/2)
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| initial_transform_axis_y = n_y * sin(alpha/2)
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| initial_transform_axis_z = n_z * sin(alpha/2)
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| </pre>
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| where <code>n=[n_x,n_y,n_z]^T</code> is the unit vecotr representing the axis of rotation and <code>alpha</code> is the angle of rotation. Example 45 degree rotation around x-axis:
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| <pre>
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| initial_transform_axis_x = 1 * sin(45/2) = 0.382
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| initial_transform_axis_y = 0 * sin(45/2) = 0
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| initial_transform_axis_z = 0 * sin(45/2) = 0
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| </pre>
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| The rotations after registration <code>final_transform_axis_x, final_transform_axis_y, final_transform_axis_z</code> can be interpreted the same way.
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| ITK provides the functions GetAxis() and GetAngle to obtain <code>[n_x, n_y, n_z]</code> and <code>alpha</code> respectively, which are calculated as follows:
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| <pre>
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| v_1 = initial_transform_axis_x
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| v_2 = initial_transform_axis_y
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| v_3 = initial_transform_axis_z
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| magnitude = sqrt(v_1^2 + v_2^2 + v_3^2)
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| n_x = v_1/magnitude
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| n_y = v_2/magnitude
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| n_z = v_3/magnitude
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| alpha = 2 * atan(magnitude/1)
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| </pre>
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| ==Statistics and Analysis==
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| ===JAGS (analysis of Bayesian models using Markov Chain Monte Carlo)===
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| See [[JAGS Usage]].
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