The "Study object" in AMIDE is used for grouping a set of related data sets and ROI's. Note that the use of the word "Study" here diverges from the traditional nuclear medicine use of the word, in which study generally connotates a single scan (or occasionally multiple but highly coupled scans) done on a single patient. A study in AMIDE is often used to group an entire experiment (several patients, several animals, whatever) into a single file. The study object itself is used mostly for storing parameters that effect all other objects stored in the study.
Similarly to the data set and ROI modification dialogs, the study modification dialog can be used to alter parameters relevant to the entire study. Right click on the name of the study in the study tree to pop-up the study modification dialog box. Parameters that can be modified are divided into the following pages.
On this page are options to alter the name and creation date of the study.
From this page, the point that the study is currently viewing can be explicitly changed. The x, y, and z dimensions are in millimeters.
The entire study (including all objects within it) can be rotated around the view center in this page. There is one dial for each of the three slice planes. The transverse dial will spin the study in the transverse plane (i.e. rotate on the z-axis). The coronal dial will spin the study in the coronal plane (i.e. rotate on the y-axis). And the sagittal dial will spin the study in the sagittal plane (i.e. rotate on the x-axis). The "reset to default" button allows the study to be rotated back to the default orientation. On the bottom of this page is a matrix showing the coordinate frame of the study with respect to the base coordinate frame.
The width of the line used to draw geometric ROIs can be altered here (1-5 pixels). This parameter is not relevant for isocontour ROI's. For isocontour ROI's, you can choose to have them draw as filled in or hollow.
Canvas layout allows you to switch the three views (transverse, coronal, and sagittal) between a linear style layout more commonly seen in PET software, and an orthogonal style layout more commonly seen in MRI software. "Maintain view size constant" allows you to pick if you want the size of the view to remain constant or not. If not checked, the size of the views shown will depend only on the data sets selected. If the checkbox is checked, the size of the views will depend on all the data sets in the study. Finally, "target empty area" is for setting the size of the empty area in the middle of the target (the crosshairs on the views when changing the view location).
This panel lists information about the study that cannot be altered. "Voxel dim" is the preferred voxel dimension, this is what the canvas will use as the "basic" voxel dimension, from which the zoom factor is relative too.