How To's
HowTo Library
- In addition to this HowTo library, much information is also available at the Scanco Medical FAQ.
- users@scanco.ch
- basser5dorf
File Transfer
HowTo: SC5019 (vivaCT) files to Sodor
$ ftp hal.kin.ucalgary.ca 220 Microsoft FTP Service Connected to hal.kin.ucalgary.ca. Name (hal.kin.ucalgary.ca:microct): hpl-nt\skboyd 331 Password required for hpl-nt\skboyd. Password: 230 User hpl-nt\skboyd logged in. FTP>
Note that you can log in as either:
- hpl-nt\skboyd
- skboyd@kin.ucalgary.ca
On the HPL network, open the window file program and type:
\\hal\FTP Home
Other options for file transfer:
$ sftp ! haven't tried it much $ scp ! doesn't work well with openvms
HowTo: FTP to douglas and donald (only in KIN network)
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:
$ douglas.kin.ucalgary.ca 220 Welcome to Dougla's FTP Service Name (douglas.kin.ucalgary.ca:ypauchard): guest 331 Password required for guest. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. FTP>
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 DISK1:[MICROCT.EVAL]IPL_FE_VM.COM on percy to include the desired analysis, e.g.:
FE_PROBLEM :== 9 !combination of 1 - 6 FE_PAR_NO :== 42 ! von Mises equivalent stress
Start the evaluation as a batch job in queue SC3309_FE
$ fem DISK3:[MICROCT.PROJECTS.DEFROM.MODELS]SHAM_A12_W12_SEG.AIM
Look at the log file SYS$SCRATCH:SHAM_A12_W12_SEG_FE.LOG during execution to verify the process.
The job is submitted using:
SUBMIT/NOPRINT/NOTIF/LOG=SYS$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
You can copy the IPL_FE_VM.COM to your project directory and use the above command to submit it.
Alternatively, FE analysis can be run interactively
$ iplfe
Extracting results
Creates a total result file called .post file.
Then, by default, it extracts one parameter (e.g. von mises stress), and produces stats file
.postlist and a colorful .aim file (_fe_par_42.aim)
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:
$ iplfe /fe_post
give .post file and write out the resulting .aim file, and it produces also the .postlist file.
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.