In order to load a new volume we must execute the program and choose the "GUI" option once on the main screen.
This option allows the user to handle a volume for analysing or editing. To load the module, we select "File" and "New Subject". This option
leads to the volume loading screen, where we can click in "Browse..." for choosing the file. Once loaded we must also choose the orientation
kind by means of the previous view. With the chosen file, we click in "Accept" to get
the volume on the screen, where it can be moved or zoomed by the use of the "Pan" and "Zoom" buttons, respectively..
Once the volume has been loaded, we can change the image cut by left-clicking on any of the three windows, each one of them showing the different orientations. Another alternative consists in scrolling the mouse up or down in order to change the current view of the cut. Using the right click, brightness can be customized. Several processing modules can be applied to a loaded volume, each one of them explained below. All the results of the different modules will be saved in a folder named as the volume under work, inside the "results" subfolder.
In order to perform a noise filtering, we go to "Tools", "Denoising" and "Run Denoising". These actions will generate two results, one of them with the filtered image (the name starts by "f"), and other containing only the residuals (name starting by "res"). A noise estimation will be also performed.
If we are only interested in noise estimation, we only need to proceed by selecting "Tools", "Denoising" and "Noise Estimation". The estimated level will be shown on screen, and no files will be generated..
For performing homogenity correction, we select "Tools" -> "Inhomogeneity Correction". A file wil be saved preceeded by "m_".
In order to perform extraction, we select "Tools" -> "Brain Extraction". Two files will appear on the work folder, one of them with the extracted brain, and other that will be used as the mask (names preceeded by "e_" and "mask_", respectively).
For classifying every tissue, we proceed by clicking "Tools" -> "Tissue Classification". This will generate the "volumes.txt" file containing all the obtained data (Total intracranial volume, cerebrospinal fluid volume, grey matter volume, white matter volume and normalized brain volume).
This process is performed by selecting "Tools"-> "Segmentation", and executes sequentially all the previus steps explained above, including the generation of the "volumes.txt" file.
For loading a mask we choose "Overlays" -> "Load Overlay", once the volume is loaded. This will show the mask placed on the desired volume. The mask transparency can be modified by "Overlays" -> "Transparency", where 0% is opaque and 100% totally transparent. The mask can be unloaded by choosing "Overlays" -> "Unload Overlay".
Once a mask is loaded, it can be edited by clicking "Editor"->"Enable Editor", which will enable the drawing tool ("Pencil" button). To draw, we left-click on the mask, with the button activated. In the same way, erase operation can be performed by right-clicking on the mask. The button options ("Size" y "Label") allow the user to select the size of the pencil and to specify a label to the mask, respectively
Once finished the mask edition, it can be saved by clicking "Editor"->"Save Mask", where the user can choose the directory and the name of the modified mask.
In order to process several files at the same time, we must click "Batch Process" on the initial screen of the application. By clicking "File"->"Select file(s)" or "File"->"Select Directory" several individual files of while directories can be selected.
The number of cases loaded will be displayed on the right part of the screen, in bold font. We must select the orientation of the cases (the same orientation is required for all of them). Under the orientation, we can select the processes to execute.
Again, the segmentation option will execute all processes sequentially.
In order to save the results we have two options:
Finally, if we want to keep only the results, and erase the intermediate files generated by the different processes, we mark the option "Remove intermediate files".
Once ready, we click "Run" in order to execute the processes. The relevant information will be shown on the Matlab's main screen.