Hello,
I would like to calculate the true physical distance between two points in an MRI. My question is the following: After processing it with the Segmentation Pipeline 2007 that creates the .trm file (subject_TO_Talairach-ACPC.trm), if I apply the linear transformation contained in the .trm file to the "cursor position" given by anatomist, do I get positions in milimeters (I really don't care much if it's the real Talairach coordinate or not)?
Thanks in advance for your help.
PS: By the way... there are a lot of links in the online documentation that lead to nowhere. Is it a problem of my web browser? thanks again.
.trm Tranformation Matrix
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riviere
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Re: .trm Tranformation Matrix
Hi,
Yes, subject_TO_Talairach-ACPC.trm transformations transform from mm coordinates to mm coordinates. You can apply it to coords given by Anatomist, if you take Anatomist coords in a view which is in the same referential as the subjects MRI volume.
But if the subject_TO_Talairach-ACPC transformation is loaded in Anatomist, and a view is set to AC/PC Talairach referential, then the coordinates displayed on that view (if the "display cursor position" option in the window menu is activated) are directly i that referential.
Thanks
Yes, subject_TO_Talairach-ACPC.trm transformations transform from mm coordinates to mm coordinates. You can apply it to coords given by Anatomist, if you take Anatomist coords in a view which is in the same referential as the subjects MRI volume.
But if the subject_TO_Talairach-ACPC transformation is loaded in Anatomist, and a view is set to AC/PC Talairach referential, then the coordinates displayed on that view (if the "display cursor position" option in the window menu is activated) are directly i that referential.
It's probably a bug in our web site... Could you please point out which links are broken ? I have found the "practical introduction to BrainVISA" on http://brainvisa.info/doc/cartointernet ... index.html and the PDF/PS docs of the disk formats on the same page. We will fix that. Are there others ?PS: By the way... there are a lot of links in the online documentation that lead to nowhere. Is it a problem of my web browser?
Thanks
Re: .trm Tranformation Matrix
Ok.
Just to be sure I understand: The coordinates given by anatomist are alredy in milimeters but I can change the origin of the coordinate system by applying the .trm transformation. This should work.
However, I find a problem when loading the Talairach referential in Anatomist. I do the following: I ask BrainVisa to open a Volume. BrainVisa then opens Anatomist and a view of the MRI in the 'Raw T1 MRI' referential. In this view the AC has as coordinates something like (121.9,129.7, 93). Then I change the referential of the view to Talairach and I also load the Talairach referential of the volume (Referential -> load) . When I put the cursor on the AC again, I get exactly the same coordinates as before (!) instead of something near (0,0,0) that would be expected. I'm using v. 3.1.6. Am I doing something wrong?
About the missing links on the documentation, I remember this one failed: http://brainvisa.info/doc/html/aims/en/ ... tials.html. I found others not working but don't remember them now. I will tell you if I encounter them again.
Thanks a lot for your help.
Just to be sure I understand: The coordinates given by anatomist are alredy in milimeters but I can change the origin of the coordinate system by applying the .trm transformation. This should work.
However, I find a problem when loading the Talairach referential in Anatomist. I do the following: I ask BrainVisa to open a Volume. BrainVisa then opens Anatomist and a view of the MRI in the 'Raw T1 MRI' referential. In this view the AC has as coordinates something like (121.9,129.7, 93). Then I change the referential of the view to Talairach and I also load the Talairach referential of the volume (Referential -> load) . When I put the cursor on the AC again, I get exactly the same coordinates as before (!) instead of something near (0,0,0) that would be expected. I'm using v. 3.1.6. Am I doing something wrong?
About the missing links on the documentation, I remember this one failed: http://brainvisa.info/doc/html/aims/en/ ... tials.html. I found others not working but don't remember them now. I will tell you if I encounter them again.
Thanks a lot for your help.
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: .trm Tranformation Matrix
Hi,
No actually you shouldn't set the Talairach referential on the volume: it is not in the Talairach ref, but has a transformation to it. If you have loaded the volume from BrainVisa, and the volume has been processed by the T1 pipeline, then everything should be setup automatically: the volume is in its own "Raw T1 MRI referential", and this ref has a transformation to Talairach. You can check it by opening the referentials window (from the settings menu of Anatomist main window) and make sure there is a link between both referentials.
Now if you set the view (and only the view) to Talairach referential, then coords displayed for this view will be Talairach, and the point (0,0,0) should be on AC.
If not, then the T1 pipeline may not have been run (or failed), the Talairach transformation (corresponding .trm) is computed at the "Talairach transformation" step of the pipeline (after the brain has been segmented).
Denis
No actually you shouldn't set the Talairach referential on the volume: it is not in the Talairach ref, but has a transformation to it. If you have loaded the volume from BrainVisa, and the volume has been processed by the T1 pipeline, then everything should be setup automatically: the volume is in its own "Raw T1 MRI referential", and this ref has a transformation to Talairach. You can check it by opening the referentials window (from the settings menu of Anatomist main window) and make sure there is a link between both referentials.
Now if you set the view (and only the view) to Talairach referential, then coords displayed for this view will be Talairach, and the point (0,0,0) should be on AC.
If not, then the T1 pipeline may not have been run (or failed), the Talairach transformation (corresponding .trm) is computed at the "Talairach transformation" step of the pipeline (after the brain has been segmented).
Right, this page has moved, actually, because some docs have been reorganized (and updated). It is now at here, but the best is to go to the general documentation page: http://brainvisa.info/documentation.html, then follow the links: user documentation, and then, AIMS help pages.About the missing links on the documentation, I remember this one failed: http://brainvisa.info/doc/html/aims/en/ ... tials.html.
Denis
Re: .trm Tranformation Matrix
That solves a lot of things.
Thanks for your help!
V
Thanks for your help!
V