hardering transforms for markus

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hardering transforms for markus

Murat Maga

Hi,


I have a set of fiducials that were collected from a volume which was under a linear transform.


Now I want to save the fiducials in the original volume coordinates, so I put the fiducials under the inverted transform and hardened it.


I want to this on a bunch of things, so I read the .tfm file into R, invert the transform and did a matrix multiplication for original RAS coordinates of fiducials.


Calculated coordinates are close but not identical.


in R: 622.1885 596.3666 857.1735
Slicer value: 627.386, 590.141, 857.088

Is this much difference normal?





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Re: hardering transforms for markus

inorton
That is a very large error and should not be considered normal. Beyond that it's hard to say. There are several possible sources of error. You may get more useful suggestions if you provide a small, reduced test case with a scene before/after, exported coordinate and transform files, and minimal R code.

(Note that you could also do batch transforms within slicer using python)


On Thu, Dec 29, 2016 at 1:18 PM Murat Maga <[hidden email]> wrote:














Hi,








I have a set of fiducials that were collected from a volume which was under a linear transform.











Now I want to save the fiducials in the original volume coordinates, so I put the fiducials under the inverted transform and hardened it.











I want to this on a bunch of things, so I read the .tfm file into R, invert the transform and did a matrix multiplication for original RAS coordinates of fiducials.











Calculated coordinates are close but not identical.










in R: 622.1885 596.3666 857.1735


Slicer value: 627.386, 590.141, 857.088





Is this much difference normal?
























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[hidden email]

http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users

To unsubscribe: send email to [hidden email] with unsubscribe as the subject

http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

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Re: hardering transforms for markus

Murat Maga
In reply to this post by Murat Maga

Turned out to be much more mundane.


Transform format presented in the .TFM file is not in the same orientation as the displayed transform matrix.

Once I rearranged it to match it, it seems to work.


I guess the close values were just coincidence.

Happy new year.

M


From: Isaiah Norton <[hidden email]>
Sent: Thursday, December 29, 2016 11:29:44 AM
To: Murat Maga; SPL Slicer Users
Subject: Re: [slicer-users] hardering transforms for markus
 
That is a very large error and should not be considered normal. Beyond that it's hard to say. There are several possible sources of error. You may get more useful suggestions if you provide a small, reduced test case with a scene before/after, exported coordinate and transform files, and minimal R code.

(Note that you could also do batch transforms within slicer using python)


On Thu, Dec 29, 2016 at 1:18 PM Murat Maga <[hidden email]> wrote:














Hi,








I have a set of fiducials that were collected from a volume which was under a linear transform.











Now I want to save the fiducials in the original volume coordinates, so I put the fiducials under the inverted transform and hardened it.











I want to this on a bunch of things, so I read the .tfm file into R, invert the transform and did a matrix multiplication for original RAS coordinates of fiducials.











Calculated coordinates are close but not identical.










in R: 622.1885 596.3666 857.1735


Slicer value: 627.386, 590.141, 857.088





Is this much difference normal?
























_______________________________________________

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

http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ

_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ