4D analysis

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4D analysis

Sando
Hello to all.

I have 10 sets of wrist CT volume (Cine 3D CT images) .

I'd lke to draw two lines in the 3D, and get the angle between two line in 3D space.

And I'd lke to obtain the changes of angles through the sets (10 sets 10 angles).

I've tried to do in the 4D module. however, it seems to be inadequaute for that.

How can I do that ?


Thanks.

Sando.
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Re: 4D analysis

Junichi Tokuda
Hi,

Currently the 4D analysis module does not have a function to observe the change of angle.
It is designed to analyze time-intensity changes in time-series images.

I'm not sure if Slicer has a function to measure an angle of two given lines.
If there isn't, I would use the Fiducials module and some external tool. Here's my suggestion:

1. Pick up three points on each image sets using Fiducials module
   (see http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.6 )
2. Export the coordinates as fcsv file from Files->Save menu. The file name should be XXXX.fcsv
3. Rename XXXX.fcsv to XXXX.csv (.fcsv is actually in CSV (comma-separated values) format)
4. Open XXXX.csv file from text editor, remove lines that begin with '#' and save
5. Open XXXX.csv file from Excel or some other spread sheet software that supports CSV file.
6. Calculate the angle between the lines defined by the three points.

If you are familiar with writing programs, you could write a simple code to do step 5 and 6.

Junichi



On Mar 21, 2011, at 9:25 AM, Sando wrote:

> Hello to all.
>
> I have 10 sets of wrist CT volume (Cine 3D CT images) .
>
> I'd lke to draw two lines in the 3D, and get the angle between two line in
> 3D space.
>
> And I'd lke to obtain the changes of angles through the sets (10 sets 10
> angles).
>
> I've tried to do in the 4D module. however, it seems to be inadequaute for
> that.
>
> How can I do that ?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/4D-analysis-tp2709876p2709876.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject



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Re: 4D analysis

inorton
For angle measurements, see Modules->Measurements->Angle Widget. Available at least in Slicer 3.6.2 and 3.6.3 (latest version).

Try this first, but if you have a lot of data to get through it may overall save time to do what Junichi suggested because it is often easier to place fiducials in the 2d planes which is not possible using the angle widget.

On Mon, Mar 21, 2011 at 11:57 AM, Junichi Tokuda <[hidden email]> wrote:
Hi,

Currently the 4D analysis module does not have a function to observe the change of angle.
It is designed to analyze time-intensity changes in time-series images.

I'm not sure if Slicer has a function to measure an angle of two given lines.
If there isn't, I would use the Fiducials module and some external tool. Here's my suggestion:

1. Pick up three points on each image sets using Fiducials module
  (see http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.6 )
2. Export the coordinates as fcsv file from Files->Save menu. The file name should be XXXX.fcsv
3. Rename XXXX.fcsv to XXXX.csv (.fcsv is actually in CSV (comma-separated values) format)
4. Open XXXX.csv file from text editor, remove lines that begin with '#' and save
5. Open XXXX.csv file from Excel or some other spread sheet software that supports CSV file.
6. Calculate the angle between the lines defined by the three points.

If you are familiar with writing programs, you could write a simple code to do step 5 and 6.

Junichi



On Mar 21, 2011, at 9:25 AM, Sando wrote:

> Hello to all.
>
> I have 10 sets of wrist CT volume (Cine 3D CT images) .
>
> I'd lke to draw two lines in the 3D, and get the angle between two line in
> 3D space.
>
> And I'd lke to obtain the changes of angles through the sets (10 sets 10
> angles).
>
> I've tried to do in the 4D module. however, it seems to be inadequaute for
> that.
>
> How can I do that ?
>
>
>
> --
> View this message in context: http://slicer-users.65878.n3.nabble.com/4D-analysis-tp2709876p2709876.html
> Sent from the slicer-users mailing list archive at Nabble.com.
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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Re: 4D analysis

Sando
In reply to this post by Junichi Tokuda
Dear, Junichi.

Many thank you very much.
The matrix information must be needed for my research.

Sincerely.

Sando.
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Re: 4D analysis

Sando
In reply to this post by inorton
Dear, Inorton.

Many thank you very much.

The angle function of 3D slicer is very good.
Thanks again.

Sincerely.

Sando.