# Trajectory calculation for stereotaxic frames

**URL:** <https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963>\
**Category:** Support\
**Created:** [October 9, 2020, 8:18pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963 "2020-10-09T20:18:29Z")\
**Posts on this page:** 20\
**Page:** 3

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [July 25, 2022, 7:57am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/42 "2022-07-25T07:57:23Z")

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Is it useful to LekSell frame?

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**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [July 25, 2022, 4:33pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/43 "2022-07-25T16:33:38Z")

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we do use:

> **[Aimsystem Stereotactic System – Micromar](https://micromar.com/en/aimsystem-stereotactic-system/)**
>
> The Aimsystem Stereotactic System TM03B, through the principle of Cartesian coordinates (X, Y and Z), reaches targets calculated with great precision.

> **[File:Stereotactic Frame TM03B Micromar.jpg](https://commons.wikimedia.org/wiki/File:Stereotactic_Frame_TM03B_Micromar.jpg)**

i don´t know if the geometry (of fiducials) are the same.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/3/d310c96fb4b5e74a2545a77a08763730bfd12a7c.png)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/0/f0c6e47a97b2142f20545c8546e5e42868db7003.png)

the sides of each square are 140 mm.-  
if not, you can modify the soft to get the proper calculations.

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [July 26, 2022, 1:47pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/44 "2022-07-26T13:47:09Z")

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thank you ! I see, it is different, leksell’s each square is 120mm。

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [July 26, 2022, 5:49pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/45 "2022-07-26T17:49:20Z")

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You can download and locally modify the extension to match your frame. Ideally, you would add a selector to allow choosing the frame.

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<div class="post-metadata">

**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [August 2, 2022, 11:38am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/46 "2022-08-02T11:38:51Z")

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you can change the stereotatic definition in script:

## [Stereotaxia](https://github.com/JBeninca/SlicerStereotaxia/tree/main/Stereotaxia)/[Recursos](https://github.com/JBeninca/SlicerStereotaxia/tree/main/Stereotaxia/Recursos)/ **Maquina\_Russell\_Brown.py**

there is a class:

class Marco\_Micromar():  
“”“Clase para encapsular datos del marco MICROMAR TM-03B”“”

which have the 9 points that reference the specific frame .

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**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 3, 2022, 8:58am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/47 "2022-08-03T08:58:29Z")

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i have some sript error on use trajectoryGuideModules  
when i press [Load Data] button ,nothing happen

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/6/46ea56f4383857f85030c7f71a1c3cf4ce301b05.png)

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**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 3, 2022, 9:26am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/48 "2022-08-03T09:26:28Z")

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> [@JBeninca](#):
>
> Marco\_Micromar(

i change the parameter from 140 to 120 , it’s also not work on leksell frame

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/d/0d7bf4f514dcddaf3c510154f0a57e96dedd3d14.jpeg)

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<div class="post-metadata">

**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [August 3, 2022, 10:28am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/49 "2022-08-03T10:28:20Z")

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Can you show me how you change the parameters?

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 3, 2022, 11:27am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/50 "2022-08-03T11:27:37Z")

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i just change the parameter from 140 to 120  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/e/1e56522e4a17d9caddb4db8d0f154a5edb9720e7.png)

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**Author:** ![Greydon\_Gilmore](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/greydon_gilmore/32/6863_2.png) [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Post date:** [August 3, 2022, 11:20pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/51 "2022-08-03T23:20:40Z")

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To correct some confusion… @jay1987 is uing my module **trajectoryGuide** and not **Stereotaxia**. @jay1987 to fix your error you need to first have your dataset in BIDS format: [https://bids.neuroimaging.io/](https://bids.neuroimaging.io/).

**trajectoryGuide** supports Leksell, BRW, and CRW frame systems.

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 4, 2022, 1:59am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/52 "2022-08-04T01:59:29Z")

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thanks,i try to use slicer to positioning Leksell headframe , i use **Stereotaxia** and **trajectoryGuide** module , both encountered different problems.  
in my process to use **trajectoryGuide** module  
1.git clone trajectoryGuideModules from github site to local  
2.follow the guide of site [https://trajectoryguide.greydongilmore.com/installation.html](https://trajectoryguide.greydongilmore.com/installation.html) to install module  
3.use slicer to load dcm files and save it to nii.gz format  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/4/14c0579c8cd846ab02c2300b66ad403ca5590c03.png)

4.use Data Import module to load the nii.gz folder

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/3/a36cf9361f097a12ef0f8727267a8a38d98890d5.jpeg)  
5.change to Frame Detection module ,and select **Leksell G LF** to Detect Frame Fiducials,after seconds computing ,i got these errors  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/4/f4e01ccca00e8cb5febfbad415f5199103ae36ea.jpeg)

the detail information bellow

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/0/f08471cb535345be3440c270ae3606ba93c79e06.png)  
@Greydon_Gilmore

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<div class="post-metadata">

**Author:** ![Greydon\_Gilmore](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/greydon_gilmore/32/6863_2.png) [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Post date:** [August 5, 2022, 2:33am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/53 "2022-08-05T02:33:36Z")

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@jay1987 do you mind sharing the frame CT volume?

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 5, 2022, 5:22am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/54 "2022-08-05T05:22:17Z")

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thanks from replying , i don’t known how to upload .rar data , it seems only support png,mp4 data uploading,would you mind leave your email for me ?

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 5, 2022, 6:51am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/55 "2022-08-05T06:51:50Z")

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You can upload data to dropbox, OneDrive, Google drive, etc. and post the download link here.

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 5, 2022, 7:04am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/56 "2022-08-05T07:04:56Z")

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> [@lassoan](#):
>
> dropbox

thanks lasso,i made a dropbox link here

> **[DataForLeksellFrame.rar](https://www.dropbox.com/s/htyh36cfca7i0jz/DataForLeksellFrame.rar?dl=0)**
>
> Shared with Dropbox

@Greydon_Gilmore

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<div class="post-metadata">

**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [August 5, 2022, 11:59am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/57 "2022-08-05T11:59:31Z")

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Dear jay1987:

Leksell and Micromar frames are different. So you can´t use the graphical issues (Stereotaxia module),  
but the light version (StereotaxiaLite) can support the Leksell with the following changes :

Also: I´ve never worked with a Leksell. I don´t know if the zero in Z is the bottom of the fiducials (I suppose it is) and I don´t know where is the zero in Y ( I assumed its in the middle of the ruler)  
fiducials is a square of 120 mm and they are separated 190

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/d/0df498473a72dfdfa4d24b16c4f82ad3868b7aeb.png)

if you take an send me a CT-scan of a free Lexsell frame, with the fiducials visibles, I could make a model of it, take the meassures and implemet a version of Stereotaxia with it.

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 5, 2022, 12:11pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/58 "2022-08-05T12:11:55Z")

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Dear JBeninca:

thanks for replying so much  
i don’t have a leksell frame data now , only have a CT-SCAN with leksell head frame sequence here

> **[DataForLeksellFrame.rar](https://www.dropbox.com/s/htyh36cfca7i0jz/DataForLeksellFrame.rar?dl=0)**
>
> Shared with Dropbox

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<div class="post-metadata">

**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [August 5, 2022, 1:36pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/59 "2022-08-05T13:36:27Z")

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Yes, i´ve downloaded it and delete the cranium and make a model of the frame. i think i could incorporate as an option in the module.  
I must check some details about the frame: have you used it?

thanks

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<div class="post-metadata">

**Author:** ![JBeninca](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jbeninca/32/10039_2.png) [@JBeninca](https://discourse.slicer.org/u/JBeninca)\
**Post date:** [August 5, 2022, 1:37pm UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/60 "2022-08-05T13:37:32Z")

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![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/7/979028b686e82ae208e528a66f6d217f2bec3b74.png)  
Leksell model from your CT scan

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<div class="post-metadata">

**Author:** ![jay1987](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jay1987/32/16183_2.png) [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Post date:** [August 7, 2022, 1:07am UTC](https://discourse.slicer.org/t/trajectory-calculation-for-stereotaxic-frames/13963/61 "2022-08-07T01:07:41Z")

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good job Beninca  
Yes, my jobs is to location the head position by leksell head frame , and use it as a component for two hospital  
can you integrate the leksell module in your Stereotaxia? it means much for us.

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