CT scan and coordinates. Help!

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CT scan and coordinates. Help!

KaraokeMary
Hello everyone,

I've been learning Fiji to analyze the data for my thesis and I need some
help. I am working with three plane CT scans (coronal, sagittal, transverse)
and measuring different skeletal elements. I have been using the reslice
tool to get all three planes to scroll independently. Unfortunately the X,
Y, Z coordinates are not global, they change with each plane view (i.e. x =
0 on the left side of the slice no matter which view I am in). I need them
to correspond in all three planes in order to do the calculations needed.
How can I do this? After days of messing around, I still can't seem to make
it happen.

Thank you in advance for any desperately needed guidance.



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Re: CT scan and coordinates. Help!

HAMZAH MARWAN BEAKAWI
Hello there,
Greetings,

Before you resliced, did you try to set the scale as global (check this option). Hopefully this might work


Heartiest Desideratum,
Yours Truly,

Hamzah M. Beakawi Al-Hashemi, S.M.ASCE

RSO | B.Sc. | M.Sc. Candidate | Civil (Geotechnical) Engineering

King Fahd University of Petroleum & Minerals (KFUPM)
College of Engineering Sciences and Applied Engineering
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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of KaraokeMary
Sent: Tuesday, February 6, 2018 7:41 AM
To: [hidden email]
Subject: CT scan and coordinates. Help!

Hello everyone,

I've been learning Fiji to analyze the data for my thesis and I need some help. I am working with three plane CT scans (coronal, sagittal, transverse) and measuring different skeletal elements. I have been using the reslice tool to get all three planes to scroll independently. Unfortunately the X, Y, Z coordinates are not global, they change with each plane view (i.e. x =
0 on the left side of the slice no matter which view I am in). I need them to correspond in all three planes in order to do the calculations needed.
How can I do this? After days of messing around, I still can't seem to make it happen.

Thank you in advance for any desperately needed guidance.



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Re: CT scan and coordinates. Help!

KaraokeMary
I did, and it sets my 1.7mm/pixel scale, but unfortunately does nothing to
the coordinate system.



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Re: CT scan and coordinates. Help!

HAMZAH MARWAN BEAKAWI
Well, try to round the pixels in the scale to a whole number and see, sometimes fractions in pixels ruin the results or the accuracy, to say the least. Wish you all the best and sorry if I wasn't able to help

Heartiest Desideratum,

Hamzah M. Al-Hashemi



From: KaraokeMary
Sent: Tuesday, February 6, 5:54 PM
Subject: Re: CT scan and coordinates. Help!
To: [hidden email]


I did, and it sets my 1.7mm/pixel scale, but unfortunately does nothing to the coordinate system. -- Sent from: https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimsva91-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttp%253a%252f%252fimagej.1557.x6.nabble.com%26umid%3D2A184684-648C-5905-BBF5-650067BBEDD5%26auth%3Dec34f7633709e8bd85e48c7fc0c92c09c079e558-13ca722b93800fce7909ae91ca4097c702de7214&data=01%7C01%7Cg201552950%40kfupm.edu.sa%7Ccf1e992891df4b4f307008d56d7175ac%7Cfe555c43628d49c6b104c175570a6776%7C1&sdata=u%2BKiz6zjjUbKJjaXOV0KtlYokmmZFitU58Wme1O4Kpc%3D&reserved=0 -- ImageJ mailing list: https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimsva91-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttp%253a%252f%252fimagej.nih.gov%252fij%252flist.html%26umid%3D2A184684-648C-5905-BBF5-650067BBEDD5%26auth%3Dec34f7633709e8bd85e48c7fc0c92c09c079e558-89e805e37eedf0f63d6021a0582458563b0ae252&data=01%7C01%7Cg201552950%40kfupm.edu.sa%7Ccf1e992891df4b4f307008d56d7175ac%7Cfe555c43628d49c6b104c175570a6776%7C1&sdata=KxMbGFiaPHpuSv5KYPEudDt%2Fv%2BbjWnHqDFAEJtG08CA%3D&reserved=0 ======================================================= This message has been analyzed by KFUPM Deep Discovery Email Inspector.


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Re: CT scan and coordinates. Help!

Jan Eglinger
In reply to this post by KaraokeMary
If I understand correctly, you'd like to have a three-pane view with
orthogonal planes, where each plane is referring to the original stack
coordinates? I.e. xy, xz and yz?

To my knowledge, this is not possible with the ImagePlus and ImageStack
classes.
The *Image > Stacks > Orthogonal Views* plugin is as far as it gets in
plain ImageJ.

You might however want to have a look at BigDataViewer [1] and what
others achieve with it, e.g. BigWarp [2] and BigCat [3].
You'll have to dive into some scripting however...

Cheers
Jan

[1]: https://imagej.net/BigDataViewer
[2]: https://imagej.net/BigWarp
[3]: https://github.com/saalfeldlab/bigcat


On 06.02.2018 05:40, KaraokeMary wrote:

> Hello everyone,
>
> I've been learning Fiji to analyze the data for my thesis and I need some
> help. I am working with three plane CT scans (coronal, sagittal, transverse)
> and measuring different skeletal elements. I have been using the reslice
> tool to get all three planes to scroll independently. Unfortunately the X,
> Y, Z coordinates are not global, they change with each plane view (i.e. x =
> 0 on the left side of the slice no matter which view I am in). I need them
> to correspond in all three planes in order to do the calculations needed.
> How can I do this? After days of messing around, I still can't seem to make
> it happen.
>
> Thank you in advance for any desperately needed guidance.
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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