[ImageJ-bugs] [Bug 888] New: Can't open Nifti files

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=888

            Bug ID: 888
           Summary: Can't open Nifti files
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Linux
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: felix.morency at gmail.com
                CC: felix.morency at gmail.com

1) Try to open a .nii.gz file (from the File → Open entry or using the LOCI
importer)
2) NullPointerException occurs

  (Fiji Is Just) ImageJ 2.0.0-rc-10/1.49d; Java 1.6.0_24 [64-bit]; Linux
3.13.0-30-generic; 27MB of 9165MB (<1%)

java.lang.NullPointerException
    at loci.formats.in.NiftiReader.initFile(NiftiReader.java:216)
    at loci.formats.FormatReader.setId(FormatReader.java:1315)
    at loci.formats.ImageReader.setId(ImageReader.java:753)
    at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:380)
    at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:362)
    at io.scif.AbstractParser.parse(AbstractParser.java:252)
    at io.scif.AbstractParser.parse(AbstractParser.java:335)
    at io.scif.AbstractParser.parse(AbstractParser.java:52)
    at io.scif.AbstractReader.setSource(AbstractReader.java:270)
    at
io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
    at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
    at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
    at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
    at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
    at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
    at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
    at
net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:136)
    at
net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:335)
    at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:152)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:662)

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.0-30-generic
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
/home/morency/software/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/morency/software/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140808140154)
Fiji: http://fiji.sc/update/ (last check:20140808140226)

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