"stacks"

[Robert J. Palmer Jr.]

Is the term "stack" in Image J translatable to that as used in
confocal or digital deconvolution microscopy?  I am struggling with
an assertion that processing of "stacks" in Image J was used to
analyze height of a feature.  Perhaps in this case the phrase
"collecting stacks of images" refers to a group of images collected
in x-y?  This is my current understanding of the term "stack" as used
in Image J - a series of related images that needn't necessarily
represent any one particular field-of-view.
--
Robert J. Palmer Jr., Ph.D.
Natl Inst Dental Craniofacial Res - Natl Insts Health
Oral Infection and Immunity Branch
Bldg 30, Room 310
30 Convent Drive
Bethesda MD 20892
ph 301-594-0025
fax [phone]

[David Hovis]

I think "stack" generally refers to a series of related images, in  
some sort of order.  Usually they have the same X-Y field and vary in  
Z, Time, Wavelength, or something else.  ImageJ is fairly agnostic  
about what you put in a stack, but if the data is confocal, then the  
"stack" probably varies in Z, Time or Wavelength.

Certainly I use ImageJ to analyze "stacks" of confocal data.  Usually  
Z-stacks in my case for topography measurements.

--David

On Jan 12, 2009, at 11:20 AM, Robert J. Palmer Jr. wrote:

> Is the term "stack" in Image J translatable to that as used in  
> confocal or digital deconvolution microscopy?  I am struggling with  
> an assertion that processing of "stacks" in Image J was used to  
> analyze height of a feature.  Perhaps in this case the phrase  
> "collecting stacks of images" refers to a group of images collected  
> in x-y?  This is my current understanding of the term "stack" as  
> used in Image J - a series of related images that needn't  
> necessarily represent any one particular field-of-view.
> --
> Robert J. Palmer Jr., Ph.D.
> Natl Inst Dental Craniofacial Res - Natl Insts Health
> Oral Infection and Immunity Branch
> Bldg 30, Room 310
> 30 Convent Drive
> Bethesda MD 20892
> ph 301-594-0025
> fax [phone]

... [show rest of quote]

[Nas-5]

Hello,

I have a set of MRI images in nii.gz format and I would like to view them in ImageJ. I've downloaded the NifTi_Analyze plugin but I can not open my images with it and I get the following error message:

-java.lang.ArrayIndexOutOfBoundsException: 8
    at Nifti_Reader.readHeader(Nifti_Reader.java:177)
    at Nifti_Reader.load(Nifti_Reader.java:124)
    at Nifti_Reader.run(Nifti_Reader.java:44)
    at ij.IJ.runUserPlugIn(IJ.java:176)
    at ij.IJ.runPlugIn(IJ.java:142)
    at ij.Executer.runCommand(Executer.java:104)
    at ij.Executer.run(Executer.java:58)
    at java.lang.Thread.run(Thread.java:619)

Is there a way to fix this or is there any other plug-in for veiwing 'nii.gz' format images?

I apprciate your your help in advance.
Nasim

[dscho]

Hi,

On Tue, 13 Jan 2009, Nasim wrote:

> I have a set of MRI images in nii.gz format and I would like to view
> them in ImageJ. I've downloaded the NifTi_Analyze plugin but I can not
> open my images with it and I get the following error message:
>
> -java.lang.ArrayIndexOutOfBoundsException: 8
>     at Nifti_Reader.readHeader(Nifti_Reader.java:177)
> [...]

You could try to unpack them first (.gz means it was zipped with gzip).

Hth,
Dscho