T1 Head stack

[Randy Seedle]

Is there a tutorial out there somewhere that explains how to build an image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
Randy Seedle

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[Michael Schmid]

Hi Randy,

there are many commands that create stacks. Here are a few:
   File>Import>Image Sequence...
   File>Import>Stack From List...
   File>Import>AVI...
   Image>Stacks>Images to Stack...
   Image>Stacks>Add Slice

See
   https://imagej.nih.gov/ij/docs/guide/index.html

It depends on where the original images come from or whether you want to
create them, e.g. in a macro.

Michael
________________________________________________________________
On 12.11.20 03:03, Randy Seedle wrote:
> Is there a tutorial out there somewhere that explains how to build an image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
> Randy Seedle
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Stein Rørvik]

The "T1 Head" example is an actual stack from a medical MRI machine.

The original data for this stack can be found here:
https://cs.uwaterloo.ca/~jorchard/mri/

It comes from a scientist who has voluntarily submitted  data from medical scans of himself. The difference between the original data and the T1 example shipped with ImageJ is that noise has been removed from the background in the sample image.

Stein


-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Randy Seedle
Sent: 12. november 2020 03:04
To: [hidden email]
Subject: T1 Head stack

Is there a tutorial out there somewhere that explains how to build an image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
Randy Seedle

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[Fred Damen]

Greetings Randy,

Are you referring to the "T1 Head (16bit)" or "T1 Head Rendering"?

I suspect that you are referring to the latter, in which case you should
google MRI surface rendering / reconstruction.  I suspect that
Horos/Osirix, or other "DICOM viewer", will perform this function.

Otherwise...

From a file format perspective neither are cine as they are just a series
of images stored in a TIF file format, i.e., they are not a series of
frames in a video file like AVI.  You can play them in a cine loop, and
convert the file format to video using ImageJ. The original images used to
produce the "T1 Head" TIF file were collected in DICOM format which stores
the physical locations of the acquired slices so that they can be
presented in correct spacial order.

Fred

On Wed, November 11, 2020 8:03 pm, Randy Seedle wrote:
> Is there a tutorial out there somewhere that explains how to build an
> image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
> Randy Seedle
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Stein Rørvik]

According to the info on the web-page I referred to in my previous post, the "T1 Head Rendering" was created using the VolumeJ plugin. I just tried it and there is a choice "Render cine-mode" which produces a stack identical to the view shown in "T1 Head Rendering" using the default options there.

Stein

-----Original Message-----
Sent: 12. november 2020 18:46
Subject: Re: T1 Head stack

Greetings Randy,

Are you referring to the "T1 Head (16bit)" or "T1 Head Rendering"?

I suspect that you are referring to the latter, in which case you should google MRI surface rendering / reconstruction.  I suspect that Horos/Osirix, or other "DICOM viewer", will perform this function.

Otherwise...

From a file format perspective neither are cine as they are just a series of images stored in a TIF file format, i.e., they are not a series of frames in a video file like AVI.  You can play them in a cine loop, and convert the file format to video using ImageJ. The original images used to produce the "T1 Head" TIF file were collected in DICOM format which stores the physical locations of the acquired slices so that they can be presented in correct spacial order.

Fred

On Wed, November 11, 2020 8:03 pm, Randy Seedle wrote:
> Is there a tutorial out there somewhere that explains how to build an
> image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
> Randy Seedle
>
> --

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[Randy Seedle]

Really what I am looking for is  something that can play a series of image files. For instance a series of Tif files.
Randy

Sent from Yahoo Mail on Android
 
  On Fri, Nov 13, 2020 at 1:06 AM, Stein Rørvik<[hidden email]> wrote:   According to the info on the web-page I referred to in my previous post, the "T1 Head Rendering" was created using the VolumeJ plugin. I just tried it and there is a choice "Render cine-mode" which produces a stack identical to the view shown in "T1 Head Rendering" using the default options there.

Stein

-----Original Message-----
Sent: 12. november 2020 18:46
Subject: Re: T1 Head stack

Greetings Randy,

Are you referring to the "T1 Head (16bit)" or "T1 Head Rendering"?

I suspect that you are referring to the latter, in which case you should google MRI surface rendering / reconstruction.  I suspect that Horos/Osirix, or other "DICOM viewer", will perform this function.

Otherwise...

From a file format perspective neither are cine as they are just a series of images stored in a TIF file format, i.e., they are not a series of frames in a video file like AVI.  You can play them in a cine loop, and convert the file format to video using ImageJ. The original images used to produce the "T1 Head" TIF file were collected in DICOM format which stores the physical locations of the acquired slices so that they can be presented in correct spacial order.

Fred

On Wed, November 11, 2020 8:03 pm, Randy Seedle wrote:
> Is there a tutorial out there somewhere that explains how to build an
> image stack (ie. cine) like the open samples item "T1 Head" in imageJ ??
> Randy Seedle
>
> --

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[Herbie]

Greetings Rand,

let's assume you have a folder with images.

1.
Go to "File >> Import >> Image Sequence", look for and choose the folder
with the images and you will get these images opened as a stack.

2.
Click on the little black triangle on the bottom left and the stack series
of images is looped through like a movie.

3.
Under "Image >> Stacks >> Animation" you will find options for the looping.

4.
You may save the stack in an AVI-container as a movie by "File >> Save As >>
AVI...". Choose the compression method and the frame rate.

5.
The saved AVI movie can now be played by most movie players available or
again be imported to ImageJ.

HTH

Herbie

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