In this step, you will select a few slices in the middle of the thigh. These slice will be the ones segmented in the next step. We will close all the slices we do not need.
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All the slices in the series |
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Selected slices in mid-thigh |
/selection_many.png)
/selection_few.png)
What the script did for you:
The "Mode ALL" is enabled, showing all the slices.
The first frame (upper left corner) is the current frame
The "DB File Management (2D)" mode interface is open.
The "Color Scheme" tool is open.
The color scheme is set to "Mix".
The "2D Frame Selection" tool is open.
The "2D Overlay" flag is set to "0" (all overlay text are removed).
What to do:
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We want an 8cm to 10cm region in the thigh starting at 2cm to 3cm above the patella.
To select the desired slices, use the following steps:
•Click on an image of your series where you see the knee and then press "Enter" to switch to the display window to "Mode One" (or click on the "One" button in the "Frame Selection" tool). Now only one image is viewed. Press the "+" key to blow the image until it fit the window.
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/file_select_1.png)
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•Press the "PgUp"/"PgDd" keys to go through the images. "PgDn" will go down through the series, but since they are sorted acording to the "Z" values in DICOM where "z" increase going toward the head, this mean that you actually go up through the leg.
•Go up until the last slice where see the patella.
•Go up between 2 to 3cm (in this case, with 8mm slices, another 3 slices).
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Patella visible on left knee |
Patella still visible |
Patella no longuer visible |
/patella_1.png)
/patella_2.png)
/patella_3.png)
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•Press "Enter" to go back to the "Display Mode All" where you see all the images. The slice we came from is the "current" slice and has a yellow border.
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/file_select_2.png)
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•In the "DB File Management (2D)" mode, click on the "Select None" button. Now all the slices are displayed in blue. (Or alternativelly, you can just click outside the images to achive the same effect.)
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/file_select_3.png)
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•Click on your "current" slice, the one with the yellow border. This curent slice will now also be selected and will be displayed in shades of grey.
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/file_select_4.png)
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•Click on the next slices to select them (going to the right and down in the display window). We want a volume 8cm to 10cm high. In this example, the slices are 8mm thick, so we will select 10 slices.
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/file_select_5.png)
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•Click on the "Close Unselected" button to close all the unselected slices. This will mark all the unselected slices for deletion.
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/file_select_6.png)
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•Clcik on the "Update DB" button to finish the process.
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/file_select_7.png)
The Interface:
We will select/unselect slices to close those that we do not need,
From the "DB File Management (2)" mode interface:
Slices can be unselected with the "Select None" button. They can be selected by clicking on the file's name, by dragging a selection box on multiple file's name. Clicking on a first file, then "Shift" click on a other file's name will select all the files in between. Also, "Ctrl" click can be used to toggle the selection of a file.
From the display window:
Slices can be unselected by clicking outside the images. The can be selected by clicking inside the images. You can drag a box and all the images touching that box will be selected. You can select a group of slices by clicking on a first one and "Shift" click on the last one of the group. You can use the "Ctrl" click to toggle a slice selection.
Note:
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If your display window is in "Mode One" (only one slice visible), then only the visible slice is selected. If you toggle between "Mode All" and "Mode One" it will automatically select all the slices (Mode All), or only the visible slice (Mode One). |