Posted by
Fred Damen on
URL: http://imagej.273.s1.nabble.com/Hyperstack-with-nz-1-problem-tp5019980p5020056.html
Greetings,
I guess my point is more ideological. I have a set of volumes of images, where
the volumes are 3D space -- a stack of slices, and the set consists of volumes
acquired using varying parameters -- frames. This is very common in MRI,
i.e., fMRI, Diffusion, ASL, etc. Some times there are cases in which we
collect only the same single slice for each parameter value. ImageJ is
handling the case of a one slice volume different than the case of multiple
slice volumes. I was wondering why this is? Do I need to add a second dummy
slice so that ImageJ treats a single slice as a volume?
In reference to 'T Project...' and 'Plot T-axis Profile...' I was referring
to averaging, etc, voxels within the volumes over the T axis. From glancing
at the ZProjector code seems to do the operation only over the slices within a
volume and not over volumes. It will repeat the operation for each frame if
requested.
It would be nice to see the change for a voxel of space over time.
Thanks,
Fred
On Thu, February 8, 2018 8:32 pm, Wayne Rasband wrote:
>> On Feb 8, 2018, at 5:22 PM, Fred Damen <
[hidden email]> wrote:
>>
>> Greetings,
>>
>> Why is a grey scale dataset with one slice per volume and many time points
>> not
>> considered a HyperStack? Is the code below, from ImagePlus, trying to tell
>> the difference between an ImagePlus without a ImageStack and an ImageStack
>> with only one entry; I can see the former being a cause to not be considered
>> a
>> Hyperstack but not the later. I am dealing with the later case.
>
> Hyperstacks have 4 or more dimensions. A stack with NC=1, NZ=1 and NT>1 has
> only 3 dimensions.
>
>> This causes me to not be able to substack my Hyperstack through the GUI.
>> Although I can do Stacks->Z Project... in the time/frame dimension with
>> (NZ=1,NT>1). Is there available tools to do 'T Project...' and 'Plot T-axis
>> Profile...' without this bug?
>
> The "Z Projectâ¦" and "Plot Z-axis Profileâ¦â commands work with
> non-hyperstacks with NT>1.
>
> -wayne
>
>
>> Code from ImagePlus:
>>
>> /** Returns 'true' if this image is a hyperstack. */
>> public boolean isHyperStack() {
>> return isDisplayedHyperStack() || (openAsHyperStack&&getNDimensions()>3);
>> }
>>
>> /** Returns the number of dimensions (2, 3, 4 or 5). */
>> public int getNDimensions() {
>> int dimensions = 2;
>> int[] dim = getDimensions(true);
>> if (dim[2]>1) dimensions++;
>> if (dim[3]>1) dimensions++;
>> if (dim[4]>1) dimensions++;
>> return dimensions;
>> }
>>
>> Thanks,
>>
>> Fred
>>
>>
>> On Fri, February 2, 2018 10:46 pm, Fred Damen wrote:
>>> Greetings,
>>>
>>> I am using hyperstacks and ran into some issues.
>>>
>>> With datasets with multiple slices(NZ>1) and multiple frames (NF>1)
>>> everything
>>> seems normal: image status bar shows z:cz/NZ t:ct/NT, and info page shows
>>> similar, two scroll bars on bottom, and, Stacks->Tools->Make Substack...
>>> present the dialog for SubHyperstackMaker.
>>>
>>> With datasets with one slice(NZ=1) and multiple frames (NF>1) there are
>>> flaws:
>>> image status bar shows n/N, info page lacks slice/frame also, one scroll
>>> bar
>>> on bottom, and Stacks->Tools->Make Substack... present the dialog for
>>> SubstackMaker and produces a stack with a 1x1 images.
>>>
>>> I suspect that ImagePlus::isHyperStack() is not recognizing single slice
>>> hyperstack properly.
>>>
>>> Thanks,
>>>
>>> Fred
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html