CSImage Tutorial v August 2000

Transcription

1 CSImage Tutorial v August 2000 To use CSImage you need to have Java2 installed. Development was done using JDK from Sun Microsystems. The program has been run on Digital Unix (Compaq Tru64 Unix), Windows, RedHat Linux (i386), and LinuxPPC (Macintosh). Only minor differences with the appearance of dialogs and the locations of window tops have been noted so far. At times Dialogs have opened with zero size, and these must be expanded prior to use. Note also that on Unix systems it is possible for a modal dialog to end up behind another window. It is usually helpful to set your window manager to require a click in the window to raise it, rather than to raise it on a mouse-enter event, so as to minimize the hiding of dialogs. Also, if you do use a mouse-enter event to raise windows, it is essential that you have a reasonable delay set for raising the window. If you have zero delay set, the Java dialogs may cause the program to freeze as some window managers get caught switching rapidly between the opening dialog and the existing on-screen window. This tutorial includes a number of preloaded CSImage format files which will be used to demonstrate the spectral functions, some non-csimage format image and 3D CSI files, which will be used to demonstrate loading external files and manipulating multidimensional data sets. Installing CSImage CSImage comes as a jar file. To install it pick the parent directory where you wish to install (you can use a standard directory like /usr/local on Unix). Unpack the files with jar xvf CSImagePre jar which will set up a directory CSImage in the parent directory. Within this there will be six additional directories. csi java strings fdf data CSImageData contains the CSImage class files in directories corresponding to the package structure contains the CSImage source files excluding string classes contains the CSImage string files which permit easy modification of the language used for on-screen display contains sample format descriptor files which are used to load non-csimage formatted files contains sample externally formatted data files for the tutorial This contains project and data files used in the tutorial

2 In addition to the directories, there is the CSImage.class file which contains the main method for the application, a Makefile which permits automatic recompilation of the source code on Unix systems, a file gnu_public_license.txt which gives the licensing terms for the program and source code, and html files providing documentation generated by javadoc. Working with Spectra in Native Format In this section you will load files containing Free Induction Decay (FID) signals which are k-space representations of spectra. The files are already in CSImage format, however no other processing has been performed. In this section you will use the basic spectral functions: zerofilling, filtering, performing FFTs, phasing, and adjusting the scales to parts per million. In addition some of the zooming features of CSImage are demonstrated. Start CSImage by invoking Java and setting a high maximum memory allowance. This is done (for 128 megabytes) with java -mx128m CSImage with the -mx128m telling java to allow the program to use 128 megabytes. If possible, use 256 megabytes for 3D work later (64 megabytes is adequate for pure spectral work). The program opens a splash screen giving information about the version of the program. Dismiss this dialog by pressing the OK button. Three windows then open, the large left window is the main window which handles data display, the upper right menu is the project menu which shows the files in the project, and the bottom right window is the history window, which shows the operations performed on the active data. Choose the About menu item from the Project Menu. A dialog opens which refers to the GNU public license under which the software is distributed. The text of the license is included in the CSImage directory. First, you will work with files already in CSImage format. Choose the Add New File menu item from the File menu in the Project Window. This will open a filechooser dialog. Double click (or

3 single click and press the Open button) on the CSImageData folder. Click on Spec512.spc in the window and press the Open button. A dialog will appear notifying you that you must give the file a new name. Press the OK button to dismiss this dialog. You will then be prompted for a file name, however you can use the same name without difficulties. In general when importing files already in CSImage format, the user will not want the file deleted by someone working on another project. The copying of the file is done to insure against this. Next repeat this process for Spec2k.spc. Two files now appear in the Project Window. Choose the Save Project menu item from the Project menu. A dialog comes up which prompts for a file name. Double click on the CSImageData folder to switch to the CSImageData directory and choose the name First.prj, then click on the Save button. Click on Spec512.spc in the Project Window and choose the Open menu item from the File menu. The figure on the previous page shows the display after CSImage opens the file. The file is actually a free induction decay (FID) signal for a phosphorous NMR spectrum. The FID is the actual measured signal from a NMR spectrometer and is the Fourier transform of the spectrum. The history window shows that you have loaded the file. This is the first item in the history for a data set in all cases. Next, choose Zerofill from the Operations menu. The figure above shows the screen with the zerofill dialog and 2048 points chosen from the popup which appears when you click on the small arrow to the right of 512. Click on 2048 and then on the OK button to zerofill the spectrum to a total of 2048 points. Next

4 choose Filter from the Operations menu. The default filter for a spectrum is a Lorentzian of 5 Hz, which is appropriate in this case, so just click on the OK button. After this the spectrum appears as in the image at the bottom of the previous page. Note that the History Window now has a list of all the operations performed. The parameters for each operation can be viewed by clicking on the dot to the left of each folder icon for operations which take a parameters. The figure shows the resulting of filtering, which is to reduce the noise in the spectrum. The points after 100 were primarily random noise so that the filter averaged them to zero. Filters are always applied in the Fourier transform space (k-space) of the object for efficiency. Next the FID is Fourier transformed by choosing the FFT menu item from the Operations menu. The result is shown in the figure above. At this point, you have loaded in an FID and then zerofilled, filtered, and Fourier transformed it to show a spectrum. The spectrum shown is reasonably processed at this point, however it can be improved by phasing. Phasing is an operation applicable to NMR spectra and takes into account phase errors introduced by the acquisition process. In order to phase the spectrum, choose the Phase menu item from the Operations menu. The figure at right shows the dialog for phasing. Use the sliders to move the constant value to approximately -11 degrees and the linear value to approximately -21 degrees. Note that all the numbers are editable, so that you could change the range of the sliders and the present values. After

5 the values are set, click the OK button to update the data. The first spectrum is now processed. This is a good time to save the present spectrum. This is done by choosing the Save menu item from the Project menu. We can also change the comment in the project window to reflect the processing. Double click on the table area to the right of the cell "Spec512.spc" in the table in the Project Window. You can now edit the comment to note that the file has been processed by adding "512->2k, Processed". Next load the second spectrum by highlighting it in the project window and choosing the Open menu item from the File menu. There are now two spectra shown on the screen. The red outline indicates the active data and all operations will be applied to it. The Project Window will highlight the file name of active data and the History Window will display the history for the active data. The active data can be changed by clicking on the data you wish to make active. Begin by flipping the Y-axis as the data is reversed from normal. This is done by choosing the Flip Y axis menu item from the Operations menu. Then zoom in on the first 250 points or so by clicking on the image around point 250 and dragging to the left edge. Then release the mouse button. The figure at right shows the operation just before the mouse button is released. Next filter the spectrum by choosing the Filter menu item from the Operations menu. This time change the filter type to Gaussian by clicking on the arrow next to "Lorentzian" and then clicking on "Gaussian". Change the filter parameter to 20, making the filter a 20Hz Gaussian. Click on the OK button and the images on screen will update, which causes them to return to an unzoomed state. Zoom in again on the first 250 points to see how they have changed. Then choose the Unzoom menu item from the Display menu to return the display to normal. Next perform a Fourier transform by choosing the FFT menu item from the Operations menu. Finally phase this spectrum as you did the previous one, this time choosing a constant phase of approximately 39 degrees and a linear phase of approximately 26 degrees. The display should now appear like the figure on the next page.

6 The final part of this section of the tutorial is to switch the point scales to parts per million (ppm). First identify which point is the peak of the lower spectrum by choosing the Show cursor lines menu item and the Show coordinates menu item from the Display menu. Then move the mouse until the vertical cursor line is on the peak of the lower spectrum. The coordinate display will help by showing the value of the peak at the point of the cursor. You should find that the peak is at point Choose the PPM scale menu item from the Display menu and enter 1024 for the reference point. Leave the ppm value at 0.0 to set the 1024 th point as 0.0 ppm. Click the OK button and the lower spectrum scale will switch to a ppm scale, as shown above.

7 Importing an Image File In this section, you will use a format descriptor file (fdf) to load an externally formatted image file. Most operations in CSImage can be applied to images, but they are more often used with spectra. As such, here we will only load an image, perform an FFT to allow us to apply a filter, and then FFT back to view the resulting image. Importing externally formatted data files requires a bit more work. The procedures encoded in CSImage are very powerful, so that most importing can be done seamlessly by creating a format descriptor file (fdf) for the specific data format you are importing. Directions for doing this are given in the CSImage Programmer's Guide. A more technical description of the methodology used for reading files with different formats is given in the CSImage Technical Notes. Importing an externally formatted data file is done in three steps. First the fdf is chosen using a filechooser dialog. Then a second filechooser dialog appears to prompt the user to choose the data file itself. Finally a filechooser dialog appears to prompt the user to name the new, CSImage formatted file. Below are the steps needed to load and manipulate a two dimensional image. If you have just completed the last part of the tutorial, choose the Remove canvas menu item from the Display menu twice, to remove the two spectra shown. If you are starting CSImage again, type java -mx128m CSImage and choose the Import File menu item from the File menu in the Project Window. The filechooser which appears has a title reminding you to choose an fdf file. Change the directory by doubleclicking on the fdf folder. Then doubleclick on the SiemensMagnImage.fdf file (or click on it and then click the Open button). Next a second filechooser appears with a title noting that you should choose the data file. Change to the data directory by first moving up to the CSImage

8 directory and then down to the brain directory. Double-click on the brhp03_imaa36.mag file. A file dialog asking for the name of the file to save will then appear. Type in the name First.img and switch to the CSImageData directory, then click the Save button. Now load the image into the program by clicking on TestImage.img in the Project Window and choosing the Open menu item from the File menu. The image should appear as shown in the figure on the previous page, although your Project Window will look different if you did not restart CSImage (i.e. your spectral files will still be shown along with the First.prj title). In general, MRI images are not processed beyond this point, however just to show the process we will filter the image. Choose the Filter menu item from the Operations menu. A dialog will appear reminding you that you must perform a Fourier transform prior to filtering. Choose the FFT menu item from the Operations menu, then choose Filter from the Operations menu. Use the popup choice menu to choose a "Cosine Squared" filter and click the OK button. Then choose the FFT menu item from the Operations menu again to return to the real space view (the image is shown above). This filter has highlighted edges. Working with Multidimensional Data Sets Finally we will import both a multidimensional spectral data file and associated images which the program will link together for display and analysis. You will first learn to load the spectral and image files so that the program can link them together. Then you will use the built-in tools to view the spectra associated with images and learn to adjust the localization of the spectra with respect to the images. Begin by starting CSImage with java -mxxxxm CSImage where XXX is 256 is you have the memory available for 128 if you do not. As before click on the OK button on the splash screen. Then choose the Import File menu item from the File menu in the Project Window. The dialog notes at the top that this is to

9 choose the fdf, so move to the fdf folder and open the FCCC CSI3D.fdf file. The next dialog prompts for the actual data file, so move back up to the CSImage directory, then into the brain directory, and open the brhp03pa_raw.mag.merged data file. You will then be prompted for a file name for the new CSImage formatted CSI3D file, so switch to the CSImageData directory and save the file as brain.csi. When the CSI3D file is loaded, it is generally preprocessed simultaneously, so a preprocessing dialog appears. For this data set, the parameters will match those used to process the full volume spectral data set, so choose the option of loading these values by pressing on the Get Values from File button. Choose the FullVolume.spc file in the CSImageData directory. The dialog will be updated with the appropriate parameters, and pressing the Preprocess button will cause the CSI3D data to be processed. Simultaneously with this processing, the program will prompt for the images, first by asking for the fdf file for images. Move to the CSImage/fdf directory and choose the SiemensMagnImage.fdf file. The program will then prompt first for the directory for the image files, which you specify by moving to the CSImage directory, then clicking once on the brain folder, and then choosing the Open button. Finally the program will prompt for the directory to store the CSImage formatted image files. Repeat the previous process by moving to the CSImage directory and clicking once on the CSImageData folder and then pressing the Open button. The program will now preprocess the CSI3D data and load the associated images. A progress dialog will follow the loading of the images and the new file names will appear in the Project Window as they are loaded. The data is now fully loaded and the program can open the CSI3D data set and appropriate associated images. Click once on brain.csi in the Project Window so it is highlighted and choose the Open menu item from the File menu. Progress bars will indicate the loading of the file and associated images, then the data will be displayed as is shown at right. The grid lines which appear over the images give the locations of the voxels with associated spectra. The highlighting indicates the nearest line to the other images shown (e.g. for the axial slice shown at the bottom left, the sagittal and coronal slices shown above lie closest to the blue lines shown over the axial slice. In order to view the spectra associated with any voxels, all that is

10 necessary is to drag across any of the images. Drag across a region of roughly 4 x 4 voxels centered on the axial image (bottom left image). The result should appear roughly as below, where a popup window showing the spectra associated with those voxels appears. In this case the spectra are extremely noisy as we have not added many acquisitions together to increase the signal to noise ratio. In addition there is imperfect phasing. In the image the third spectra in the second row has been highlighted by clicking on it. In addition, these spectra can be zoomed just as a single spectrum can by dragging across a spectrum. Finally, any individual spectrum can be captured to a file for study as a single spectrum. To do this, highlight the spectrum by clicking on it and then press the "Capture spectrum" button. A dialog appears noting that you must save this as a new file. Press the OK button and then save the new file as CaptSpec.spc in the CSImageData directory. Finally save the entire set of files and the project by choosing the Save Project menu item from the Project menu. Save the project as Brain.prj in the CSImageData directory. CSImage also permits the exploration of the image data set. Click on the lower left axial image if it is not the active image (red highlight around the edge) to make it active. Then choose the Next image menu item from the CSI3D menu. Repeat this two more times to move down through the axial slices. Also note that the grid line marked in blue moves as is appropriate as you switch images. Since the images are not exactly aligned with the three dimensional grid defined by the spectra, the nearest voxel will not shift with each image (in fact for this data set there are more image slices in each direction than spectral voxels). It is often desirable when working with these spectral data sets, where spectra arise from reasonably large volumes, to move the center of the voxel so that it is aligned with some anatomical feature. To demonstrate this, choose the Voxel shifting menu item from the CSI3D menu. A dialog will open. (On some Java implementations, the images will not appear square. This can be fixed by dragging the bottom of the window until the images are square.) Use the sliders to set the y shift to voxel and the z shift to 0.38 voxel. This will center the ventricle feature in the upper left slice (sagittal image) within a single

11 voxel. Press the Accept button and the voxel shifting will be performed (this may take a moment and the progress bar is not yet implemented in this version). The screen should then appear as below. This completes the tutorial. If you wish to save this project, choose the Save Project menu item from the Project menu.