How To Process The PET/CT Data On Your Own PC: (Quick Manual)

[Quick Manual]
How to process the PET/CT data on your own PC

Normally, after the PET data have been acquired on VISTA microPET system (and if necessary, the corresponding CT data on XSPECT micro CT system), the reconstructed PET and CT data (as well as co-registered data if being requested) will be generated and uploaded onto the Terastation by the technicians. To view and process such results, you can copy the data from the Terastation and use open source programs ImageJ and Amide to do what you want. Preparation Step1. Log in the Terastation Click Start/Run or Win+R, and type \\10.16.96.95 to login. Or just type this IP address in the address bar of any browser to login. Input the username and password if its your first time to access. Please contact Jianhua ([email protected] ) if you dont know the password of your account or you have any questions on the Terastation. Step2. Download ImageJ and Amide to your own PC ImageJ and Amide have been copied onto the terastation \\10.16.96.95\Share\Software . [Remark] 1. You MUST copy the whole folder of ImageJ onto your C:\ disk, and then you can directly run it by clicking C:\ImageJ\ImageJ without installation. 2. Before you run the amide-0.8.13-2_install.exe installer, you MUST run GTKRuntime-Environment and gtk+-2.6.9 first and copy libxml2.dll into C:\Windows\System32. 3. You can find much more information on the websites: ImageJ: http://rsb.info.nih.gov/ij/ Amide: http://amide.sourceforge.net/ Practice Step3. Process reconstructed PET data in Amide Copy the reconstructed PET data (*.hdr & *.img) from the Terastation to your own PC. Since Amide only supports only version 3.3 interfiles and the PET data are written as version 4.0, there is an incompatibility problem. Therefore you should modify the interfile slightly as follows: open the header file (*.hdr) with Notepad, modify the line with version of keys := 4.0 to be version of keys := 3.3, and then save it. Run Amide and click the menu File/import file (specify)/interfile3.3, select the interfile to open. Some warnings will appear on the screen, but they can be ignored.
Consult the AMIDE User's Manual for the operations to realize your goal. http://amide.sourceforge.net/help/C/index.html Step4. View or transfer the CT data in ImageJ The reconstructed CT data are saved as 512 or 256 transaxial slices. You can view the slices by clicking the menu file/import/raw in ImageJ, and then selecting one slice at random. In the pop-up window, set Image Type=16-bit Signed; Width=512; Height=512; Offset=0; Number of Images=1; Gap=0; make sure little-endian byteorder is checked and check the Open All Files in Folder box. The program then will load all 512 CT slices. (If any additional files are present in the folder, they may create extraneous slices which must be deleted). In order to transfer the slices into ONE interfile image (*.hdr & *.img), just click plugins/NucMed/save as interfile. Give a meaningful filename for the result. Note that this procedure requires the NucMed plugin which is contained in the ImageJ package on the Terastation. Improvement Step5. View and adjust the co-registered result in Amide As mentioned in Step 3, you should modify the interfile header of the PET data with Notepad first. Open the co-registered CT and PET interfiles successively by clicking the menu File/import file (specify)/interfile3.3. Compared with VISTA system, Amide uses different method to load the images, so you should adjust the CT data as follows so that CT and PET can be co-registered correctly in Amide: Open the Modification Dialog by right-clicking the CT data in the Study tree, modify the voxel size to the exact same values as the PET data, and in the sheet named Rotate click the button invert axis of z axis. After adjusting the contrast of the both data sets, you will find the fused results. Indeed, you can not only analyze the co-registered data in Amide but also do the coregistration in Amide by yourself if you have transferred the CT slices into interfiles. Step6. Create 2-D image or 3-D movie for your presentation Save current image as 2-D image in all kind of image format o ImageJ: Click File/Save as o Amide: Click Flie/Export view Adjust the contrast o ImageJ: Click Image/Adjust/Brightness_contrast o Amide: Right Click the data icon in the study tree, and select the tab colormap/threshold Draw ROI 2
o ImageJ: Use all kinds of icons below the menu o Amide: Click Edit/Add ROI Analyze the image or ROI o ImageJ: Click Analyze/ measure OR histogram OR plot profile o Amide: Click Tools/ generate line profile OR calculate ROI Generate 3-D movie o ImageJ: Click File/Save as/AVI o Amide: Click View/volume rendering, and click Execute Decrease the image size o ImageJ: Click Image/Crop OR Plugins/Stack/slice remover o Amide: Click Tools/Crop Active data set The above is some examples, ImageJ and Amide provide much more powerful tools and functions to help the user the realize all kinds of processing and analysis.
Complement Step 7. Concatenate the CT images from multi-bed scanning. In order to get the whole body image of rat, we normally have to scan 2~4 bed positions due to the limited FOV size of the microCT and micro PET. For PET data, the VISTA system concatenates the images automatically, while for CT data, this job has to be done manually to date. 1) Open the reconstructed CT data for the first bed position in ImageJ as in Step 4. 2) Use Image/Crop or Stack/slice remover to decrease the image size. Record the parameters (Selection range, slice interval, etc.) 3) (Optional) Normally we can delete first and last tens of the CT slices because of strong wrap-around artifacts. Click Plugins/Stack/stack maker, and input for example 51-462 to delete the first and last 50 slices. If the number of slices was 512 originally, this will leave 412. 4) Open the second bed position data and do the above two operations 5) Select the last slice of the first-bed image, and then scroll the second-bed image slowly to find the corresponding same position slice, eg. Slice 47. 6) Make sure the second-bed data are in the current window, click Plugins/Stack/stack maker, input e.g. 48-462. 7) Click Plugins/Stack/concatenator, select the first-bed image in the first list-box, and the second-bed image in the second one. Click OK 8) Then the concatenated image for first and second beds is generated. Repeat 1)~7) for the third bed or fourth bed. (Optional) the following 3 steps are specially for preparation of registration on VISTA PET system. 9) Click the menu image/properies, and set unit of length=mm; pixel width= pixel height= voxel depth=0.17 10) Click the menu process/math/subtract, and set value= 32767
11) Click the menu image/adjust/brightness and click reset to see the adjusted result 12) Click the menu plugins/NucMed/save as interfile, give a meaningful name for the new file. The results are a pair of file with the same file name but different extended names like ***.hdr and ***.img.

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[Quick Manual]

How to process the PET/CT data on your own PC

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