Autosegmentation

Defining the tumor sizes and locations can be done automatically as well as manually via ROIs. The automatic mode is done under the nifti tab (see demo ). Another demo of Nifti in external programs. (There is an additional segmentation using 3D Counter).

You need to define where the files will be stored on disk (one time operation).
Note use tmp file, if not use:. This allows the use of temporary files instead of the defined location. This may be useful on some Mac computers. If you need to find the files manually, go to the OS defined tmp directory and look for a folder whose name begins with nifti. This folder will be deleted every time a shut down is performed on the computer.

Since the calculation can be fairly lengthy, it is generally advised to use Use the axial and coronal views to define limits for the search. The search for tumors will be confined to the defined volume. Then press the button Press to run, and be patient. When the calculation has completed the button will display Done with the calculation time in parenthesis.

Note that for large PET matrix sizes the calculation may take too long to be useful. For 144x144 it is still OK, but above this, it can be quite lenghty. Using Use the axial and coronal views to define limits for the search can easily make the calculation 10 times faster, making larger matrix sizes feasible. In the example below, it only makes sense to compute the abdominal area. First the axial view is shown with its bounding rectangle:

Then the coronal view is shown, again with its bounding rectangle.

The calculation is divided into 2 parts: the initial definition of the tumor points and a growing of these points into surrounding areas. This is all automatic but you will see on the Fiji status bar messages as to what is occurring. For the growing part a new window will briefly be displayed with the surrounding points. When all is finished the Done button will be displayed.

Checking the results

It should be noted that the calculation is not fool proof. There can be both false positives and false negatives. First you should switch to the ROI tab and check the blue dots display . Check Show all. Make sure the MIP is displayed. This will give you an overall idea of what has been chosen, what has not been chosen, and how big the ROIs are.

False positives

Next you release Show all and use the spinner to go through the ROIs one by one. Perhaps the ROI is too big for your estimation of the tumor size. Perhaps it includes a kidney or something which isn't a tumor. It is now you who is in control and not the computer, and you need to eliminate any false positives. To delete a given ROI press the trash button. On the first delete you will be given a warning message saying that you are about to delete a ROI.

Continue with the spinner and go through all of the ROIs which were automatically defined and delete any ones which you do not agree with. While you are going through them you may want to label the ROIs with a meaningful label from the drop down combo box under Show all. For details, see Label . You may also want check use SUV limits to further filter what is included in the blue dots.

False negatives

After you have removed all which is not acceptable, you may want to check again Show all to get another overview of what is included. If tumors a not included you will need to use manual ROIs.

An important point to be noted is you have to do the autosegmentation first, before any manual ROIs are defined.

If additional ROIs need to be manually included, you will almost certainly need use SUV. For small tumors you can use the sphere option. Otherwise don't check the sphere and use the usual irregular ROIs. Even if you need to define manual ROIs, the autosegmentation can save you time by doing the lion's share of the work.

Saving your results

Don't forget to save your results by pressing the Save button. The details are here and here. A dialog will appear asking where to save the results. Generally it is fixed place on disk, so that you only need to define it once. When you want to display your results in a spread sheet, this is the place to get the input data.

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