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| __TOC__
| | #REDIRECT [[Main Page]] |
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| =HowTo Library=
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| :In addition to this HowTo library, much information is also available at the [http://www.scanco.ch/cgi-bin/scanco.pl?menu=support&site=faq Scanco Medical FAQ].
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| :*users@scanco.ch
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| :*basser5dorf
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| ==File Transfer==
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| ===HowTo: SC5019 (vivaCT) files to Sodor===
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| <pre>
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| $ ftp hal.kin.ucalgary.ca
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| 220 Microsoft FTP Service
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| Connected to hal.kin.ucalgary.ca.
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| Name (hal.kin.ucalgary.ca:microct): hpl-nt\skboyd
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| 331 Password required for hpl-nt\skboyd.
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| Password:
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| 230 User hpl-nt\skboyd logged in.
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| FTP>
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| </pre>
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| Note that you can log in as either:
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| *hpl-nt\skboyd
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| *skboyd@kin.ucalgary.ca
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| On the HPL network, open the window file program and type:
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| <code>
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| \\hal\FTP Home
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| </code>
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| Other options for file transfer:
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| <pre>
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| $ sftp ! haven't tried it much
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| $ scp ! doesn't work well with openvms
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| </pre>
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| ===HowTo: FTP to douglas and donald (only in KIN network)===
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| There are FTP servers running on douglas and donald for file transfer WITHIN the KIN network only, e.g. percy or your PC. If you are connecting from home, establish a PPTP VPN connection to nt-hpl first to be virtually in the KIN network. Access from scanners at the hospital (VivaCT) is not possible at the moment. Use user guest and correpsonding password for login to either douglas.kin.ucalgary.ca or donald.kin.ucalgary.ca:
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| <pre>
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| $ douglas.kin.ucalgary.ca
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| 220 Welcome to Dougla's FTP Service
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| Name (douglas.kin.ucalgary.ca:ypauchard): guest
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| 331 Password required for guest.
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| Password:
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| 230 Login successful.
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| Remote system type is UNIX.
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| Using binary mode to transfer files.
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| FTP>
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| </pre>
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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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