DICOM image stack

Posted by FrancescoPiasentini on Jan 12, 2017; 3:00pm
URL: http://imagej.273.s1.nabble.com/DICOM-image-stack-tp5017868.html

Dear All,
I'm a new ImageJ user.

I'm working on CT dataset, both from medical scanners (DICOM) and from industrial scanner (in Volume Graphics proprietary format: .vgl).

When converting .vgl to DICOM, I have an image sequence that I can import as Image Sequence or Bio-formats in FIJI (up-to-date, WIN 10) the latest with a flag in "Group files with similar names".

Then I can execute the 3D volume viewer.

Then I would like to generate a DICOMDIR file that help a DICOM viewer to interpret all my .dcm files as a single serie.

Tudor is not working with my Fiji version:

(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 1437MB of 98195MB (1%)
 
java.lang.NoClassDefFoundError: lu/tudor/santec/dicom/anonymizer/SimpleAnonPanel
        at java.lang.Class.getDeclaredConstructors0(Native Method)
        at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
        at java.lang.Class.getConstructor0(Class.java:3075)
        at java.lang.Class.newInstance(Class.java:412)
        at ij.IJ.runUserPlugIn(IJ.java:215)
        at ij.IJ.runPlugIn(IJ.java:181)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: lu.tudor.santec.dicom.anonymizer.SimpleAnonPanel
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 9 more

Thanks to all!! ImageJ seems to be a promising application!

--

An example of the DICOM header generated by VGStudioMAx:

 BitsPerPixel 16
 DimensionOrder XYCZT
 IsInterleaved false
 IsRGB false
 LittleEndian true
 PixelType uint16
 Series 0 Name Series 0
 SizeC 1
 SizeT 1
 SizeX 648
 SizeY 306
 SizeZ 1714
0002,0002 Media Storage SOP Class UID #1 1.2.840.10008.5.1.4.1.1.2
0002,0003 Media Storage SOP Instance UID #1 2.25.939231546697130062711189260633828571005
0002,0010 Transfer Syntax UID #1 1.2.840.10008.1.2.1
0002,0012 Implementation Class UID #1 1.2.276.0.7230010.3.0.3.5.4
0002,0013 Implementation Version Name #1 OFFIS_DCMTK_354
0008,0016 SOP Class UID #1 1.2.840.10008.5.1.4.1.1.2
0008,0018 SOP Instance UID #1 2.25.939231546697130062711189260633828571005
0010,0010 Patient's Name #1 Volume 1
0010,0020 Patient ID #1 volume
0020,000d Study Instance UID #1 2.25.1669579281968996690913143969303353717994
0020,000e Series Instance UID #1 2.25.959810748906388118909445991464943427463
0020,0011 Series Number #1 1
0020,0012 Acquisition Number #1 1
0020,0032 Image Position (Patient) #1 0.500000\0.500000\0.521000
0020,0037 Image Orientation (Patient) #1 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000
0028,0002 Samples per pixel #1 1
0028,0004 Photometric Interpretation #1 MONOCHROME2
0028,0010 Rows #1 306
0028,0011 Columns #1 648
0028,0030 Pixel Spacing #1 0.042000\0.042000
0028,0100 Bits Allocated #1 16
0028,0101 Bits Stored #1 16
0028,0102 High Bit #1 15
0028,0103 Pixel Representation #1 0
0028,1052 Rescale Intercept #1 0.000000
0028,1053 Rescale Slope #1 1.000000
Header information