Freehand selections with Clear Outside to a specific value

[Kischell, Eric R., M.S.]

Hello,
I am employing the latest version of Fiji / ImageJ.
After importing a Nifti volume representing CT Hounsfield (HU) values...

I am utilizing Freehand selections with Clear Outside.
I wish to set the outside pixels in each slice to a negative HU value like -1000.
Is there an Option to set the outside fill value in this manner?
thx e.-

Eric Kischell (keesh)
Senior Analyst
Custom Application Development Unit
Mayo Clinic, 200 First Street SW, Rochester MN 55905
Email: [hidden email]<mailto:[hidden email]>
Life Plan:
To improve the quality of life for all mankind through better pattern recognition techniques.


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[Herbie]

Good day Eric,

I assume that your images or stacks are 32bit because otherwise ImageJ
won't display negative values.

For setting the outside to a given value you could invert the selection
(Edit >> Selection >> Make Inverse) and then set the now selected area
to your liking (Process >> Math >> Set...).

You may use the macro recorder (Plugins >> Macros >> Record...) to
record the sequence of actions and use the resulting macro for future
processing.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 23.11.19 um 18:17 schrieb Kischell, Eric R., M.S.:

> Hello,
> I am employing the latest version of Fiji / ImageJ.
> After importing a Nifti volume representing CT Hounsfield (HU) values...
>
> I am utilizing Freehand selections with Clear Outside.
> I wish to set the outside pixels in each slice to a negative HU value like -1000.
> Is there an Option to set the outside fill value in this manner?
> thx e.-
>
> Eric Kischell (keesh)
> Senior Analyst
> Custom Application Development Unit
> Mayo Clinic, 200 First Street SW, Rochester MN 55905
> Email: [hidden email]<mailto:[hidden email]>
> Life Plan:
> To improve the quality of life for all mankind through better pattern recognition techniques.
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Kischell, Eric R., M.S.]

Thanks, Herbie.
Your suggestion will help me crop for input into a deep learning algorithm.
e.-


-----Original Message-----
From: Herbie [mailto:[hidden email]]
Sent: Saturday, November 23, 2019 11:28 AM
To: [hidden email]
Subject: [EXTERNAL] Re: Freehand selections with Clear Outside to a specific value

Good day Eric,

I assume that your images or stacks are 32bit because otherwise ImageJ
won't display negative values.

For setting the outside to a given value you could invert the selection
(Edit >> Selection >> Make Inverse) and then set the now selected area
to your liking (Process >> Math >> Set...).

You may use the macro recorder (Plugins >> Macros >> Record...) to
record the sequence of actions and use the resulting macro for future
processing.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 23.11.19 um 18:17 schrieb Kischell, Eric R., M.S.:

> Hello,
> I am employing the latest version of Fiji / ImageJ.
> After importing a Nifti volume representing CT Hounsfield (HU) values...
>
> I am utilizing Freehand selections with Clear Outside.
> I wish to set the outside pixels in each slice to a negative HU value like -1000.
> Is there an Option to set the outside fill value in this manner?
> thx e.-
>
> Eric Kischell (keesh)
> Senior Analyst
> Custom Application Development Unit
> Mayo Clinic, 200 First Street SW, Rochester MN 55905
> Email: [hidden email]<mailto:[hidden email]>
> Life Plan:
> To improve the quality of life for all mankind through better pattern recognition techniques.
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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