# Probe position and IJK\_RAS coordinates

**URL:** <https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169>\
**Category:** Support\
**Created:** [February 6, 2024, 3:06pm UTC](https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169 "2024-02-06T15:06:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![alessandro\_um](https://avatars.discourse-cdn.com/v4/letter/a/ac91a4/32.png) [@alessandro\_um](https://discourse.slicer.org/u/alessandro_um)\
**Post date:** [February 6, 2024, 3:06pm UTC](https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169/1 "2024-02-06T15:06:33Z")

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Hello,  
I am learning the ropes with orienting dicoms, so I am using some well known softwares as a ground of truth, among them I’m using Slicer.  
Through math formulas I obtained the same data found under Volume Information (origin and rotation matrix).  
What I am struggling to catch are the points coordinates shown in Data Probe that show up when moving the cursor [CT.xxxxxx (coord1, coord2, coord3)], this are the coordinates in unscaled dicom coordinates with RAS orientation?  
Given a point P\_ijk (should be in not oriented raw data coordinates right?), and having the IJK\_TO\_RAS\_matrix, to obtain the probe position I should do: IJK\_TO\_RAS\_direction\_matrix \* P\_ijk?

As an example, I have a CT dicom of a patient in a prone position, the header data are:  
image\_patient\_position = [134.716796875, 313.716796875, -78.5]  
image\_orientation\_patient = [-1,0,0,0,-1,0]  
rows = columns = 512  
spacing = [0.566, 0.566]  
calculated\_spacing\_between\_slices = 0.7  
n\_slices = 177  
Extent = [0, 512, 0, 512, 0, 177]

In Slicer upon loading the dicom i have:  
the origin in [-134.716796875, -313.716796875, -78.5] and  
the IJKtoRAS\_direction\_matrix =  
[1.0, 0.0, 0.0]  
[0.0, 1.0, 0.0]  
[0.0, 0.0, 1.0].  
I have the same numbers using my formulas, so to obtain the ijk position of the upper\_left\_corner Pnt[0.0, 0.0, 0.0] in IJK i did [IJKtoRAS\_direction\_matrix \* Pnt] and obviously I get the same point as the rotation matrix is an Identity, but in probes coordinates it’s [512, 512, 0] and not [0, 0, 0].  
What am I missing?

 ![probe_position](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/1/41a5ec71d6ffb0080f5419ca1fbdb495fef85ee8.png)

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<div class="post-metadata">

**Author:** ![alessandro\_um](https://avatars.discourse-cdn.com/v4/letter/a/ac91a4/32.png) [@alessandro\_um](https://discourse.slicer.org/u/alessandro_um)\
**Post date:** [February 6, 2024, 4:21pm UTC](https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169/2 "2024-02-06T16:21:17Z")

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Maybe the rotation around the corner (origin in IJK) can be misleading as the rotation is done around the origin, in my tests I evaluate the rotation of the points forming the bounding box having the same extent as the volume.