Editing Finite Element Modelling (section)

==Create Original AIM File from Raw Data==

After you finish scanning, wait for the reconstruction to be completed. In a VMS terminal, type in "mcutout" to open the uCT Evaluation Program. If you are doing this remotely, open Terminal and connect to SCEVAL with the "invivo" username using ssh:

<pre>
$ ssh -l invivo -X sceval.ucalgary.ca
</pre>

Then type in "mcutout" once it has logged you in.

Open the desired measurement, and use the selection options on the left to create your contours. Click "Tasks" --> "Contouring" for more contouring options (if you want to apply the contours to all slices, for example).

Then Click "Tasks" --> "Evaluation 3D". Select a Task/Evaluation (just choose the top one on the list unless you are segmenting this sample for a second time) and decide on the optimal lower threshold, sigma, and support (leave upper threshold at 1000). Now save the gobj file by going to "File" --> "Save GOBJ as", selecting the required GOBJ file and clicking "OK". Now click "Start Evaluation" and wait for the evaluation to be completed. You may close uCT Evaluation Program now.

In the VMS terminal, go to the sample's directory. For example, if it was sample number 4800 and measurement number 10950, type:

<pre>
$ cd ud *4800 10950
</pre>

In here, you will find 7 files, two of those being the GOBJ file and the AIM file. They will have file names such as:

<pre>
C0010659_1.GOBJ and
C0010659_1.AIM (you do not need the *_SEG.AIM file).
</pre>


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