Fwd: Slicer questions

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Fwd: Slicer questions

reckbo
Hi everyone,

Dr. Tejas Sankar is trying to use Slicer for a particular registration
problem that I hope someone can help with.  In short he would like to
register a post-op CT to a pre-op MRI but then also have those
registered to Talairach or MNI space.  I've included his complete
description of the problem below.

Thanks in advance,
Ryan

---------- Forwarded message ----------
From: Tejas Sankar <[hidden email]>
Date: Wed, Oct 26, 2011 at 1:26 PM
Subject: Re: Slicer questions
To: Ryan <[hidden email]>


Hi Ryan,
Thanks very much for offering to help with this. Perhaps I should
start by saying that I am a relative novice when it comes to using
Slicer, and at the best of times I'm a simple surgeon, so I'm
essentially looking for cookbook solutions. Furthermore, I'm trying to
solve this problem for a group of surgeon end users whose literacy
with neuroimaging is highly variable.
That out of the way, let me just restate the problem. I have a
pre-operative MRI scan and a post-operative CT scan.  The post-op scan
contains electrodes which are inserted into the brain during surgery.
The first issue is to fuse (register) the post-operative CT to the
pre-op MRI, to be able to visualize the relationship between
anatomical structures--on the MRI--and electrode positions on the CT.
The second issue is that I want to be able to transform both the MRI
and fused CT into Talairach or MNI space, and subsequently determine
the coordinates of the electrodes in the brain, by navigating over the
electrodes with the mouse cursor.
Using the "Expert Automated Registration" module--by my understanding
a combination of a linear and a non-linear transform--I have
consistently been able to get a good-quality registration of the
post-op CT with the pre-op MRI. However, I do not know how to then
transform the MRI or CT into Talairach or MNI space using Slicer,
allow me to then navigate and determine the electrode coordinates.
It is worth mentioning that none of the other Slicer registration
algorithms seem to produce satisfactory co-registrations of our
particular CT and MRI scans. I wonder if this is due to distortion of
landmarks by electrode artifact.
Hopefully what I'm asking is clear; any help you could provide would
be greatly appreciated.
Regards, and thanks again,
Tejas Sankar, MD, FRCSC Neurosurgery
University of Toronto
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slicer-users mailing list
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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
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Re: Fwd: Slicer questions

Dominik Meier
Hi Ryan

>From the description below it sounds like the CT-MRI registration is already quite successfully addressed in Slicer. We can also recommend the BRAINSfit module as contingency if the ExpertAutomated one should not succeed.  Most common reason for registration failure is distracting image content (the electrodes) and large differences in the field of view that create unmatchable image content. Masking is a good remedy for that, supported by several (albeit not all) Slicer registration tools. Another important step is the initial position, if the two scans are far apart, a rough manual initial alignment may be necessary prior to running the automated registration. A tutorial on manual alignment can be found here:

http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C16
http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training
http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ

You can find related example cases here:

http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C12
http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C18

Finally there is a large FAQ section on registration that also covers some of these points:
http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ

I'm not aware of dedicated Talairach registration in Slicer. So bringing the fused data into a common MNI/Talairach space would entail a second, separate nonrigid registration. First align the pre-op MRI with the atlas via an affine + nonrigid BSpline and then apply that transform to the CT. Use one of the dedicated resamplers:

http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6
or
http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSResample


Best,
Dominik


On Oct 31, 2011, at 11:02 AM, Ryan wrote:

> Hi everyone,
>
> Dr. Tejas Sankar is trying to use Slicer for a particular registration
> problem that I hope someone can help with.  In short he would like to
> register a post-op CT to a pre-op MRI but then also have those
> registered to Talairach or MNI space.  I've included his complete
> description of the problem below.
>
> Thanks in advance,
> Ryan
>
> ---------- Forwarded message ----------
> From: Tejas Sankar <[hidden email]>
> Date: Wed, Oct 26, 2011 at 1:26 PM
> Subject: Re: Slicer questions
> To: Ryan <[hidden email]>
>
>
> Hi Ryan,
> Thanks very much for offering to help with this. Perhaps I should
> start by saying that I am a relative novice when it comes to using
> Slicer, and at the best of times I'm a simple surgeon, so I'm
> essentially looking for cookbook solutions. Furthermore, I'm trying to
> solve this problem for a group of surgeon end users whose literacy
> with neuroimaging is highly variable.
> That out of the way, let me just restate the problem. I have a
> pre-operative MRI scan and a post-operative CT scan.  The post-op scan
> contains electrodes which are inserted into the brain during surgery.
> The first issue is to fuse (register) the post-operative CT to the
> pre-op MRI, to be able to visualize the relationship between
> anatomical structures--on the MRI--and electrode positions on the CT.
> The second issue is that I want to be able to transform both the MRI
> and fused CT into Talairach or MNI space, and subsequently determine
> the coordinates of the electrodes in the brain, by navigating over the
> electrodes with the mouse cursor.
> Using the "Expert Automated Registration" module--by my understanding
> a combination of a linear and a non-linear transform--I have
> consistently been able to get a good-quality registration of the
> post-op CT with the pre-op MRI. However, I do not know how to then
> transform the MRI or CT into Talairach or MNI space using Slicer,
> allow me to then navigate and determine the electrode coordinates.
> It is worth mentioning that none of the other Slicer registration
> algorithms seem to produce satisfactory co-registrations of our
> particular CT and MRI scans. I wonder if this is due to distortion of
> landmarks by electrode artifact.
> Hopefully what I'm asking is clear; any help you could provide would
> be greatly appreciated.
> Regards, and thanks again,
> Tejas Sankar, MD, FRCSC Neurosurgery
> University of Toronto
> _______________________________________________
> 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: Fwd: Slicer questions

madanrao
Hello,

You can use Slicer3 image's appropriate co-ordinates fed into BioImage suite to obtain its talairach co-ordinates.

http://www.bioimagesuite.org/Mni2Tal/yale_mni_2_tal.pdf

http://www.bioimagesuite.org/doc/node7.html#SECTION02540010000000000000

I hope this helps.

AM Mohan Rao


On Tue, Nov 1, 2011 at 1:08 AM, Dominik Meier <[hidden email]> wrote:
Hi Ryan

>From the description below it sounds like the CT-MRI registration is already quite successfully addressed in Slicer. We can also recommend the BRAINSfit module as contingency if the ExpertAutomated one should not succeed.  Most common reason for registration failure is distracting image content (the electrodes) and large differences in the field of view that create unmatchable image content. Masking is a good remedy for that, supported by several (albeit not all) Slicer registration tools. Another important step is the initial position, if the two scans are far apart, a rough manual initial alignment may be necessary prior to running the automated registration. A tutorial on manual alignment can be found here:

http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C16
http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training
http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ

You can find related example cases here:

http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C12
http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C18

Finally there is a large FAQ section on registration that also covers some of these points:
http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ

I'm not aware of dedicated Talairach registration in Slicer. So bringing the fused data into a common MNI/Talairach space would entail a second, separate nonrigid registration. First align the pre-op MRI with the atlas via an affine + nonrigid BSpline and then apply that transform to the CT. Use one of the dedicated resamplers:

http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6
or
http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSResample


Best,
Dominik


On Oct 31, 2011, at 11:02 AM, Ryan wrote:

> Hi everyone,
>
> Dr. Tejas Sankar is trying to use Slicer for a particular registration
> problem that I hope someone can help with.  In short he would like to
> register a post-op CT to a pre-op MRI but then also have those
> registered to Talairach or MNI space.  I've included his complete
> description of the problem below.
>
> Thanks in advance,
> Ryan
>
> ---------- Forwarded message ----------
> From: Tejas Sankar <[hidden email]>
> Date: Wed, Oct 26, 2011 at 1:26 PM
> Subject: Re: Slicer questions
> To: Ryan <[hidden email]>
>
>
> Hi Ryan,
> Thanks very much for offering to help with this. Perhaps I should
> start by saying that I am a relative novice when it comes to using
> Slicer, and at the best of times I'm a simple surgeon, so I'm
> essentially looking for cookbook solutions. Furthermore, I'm trying to
> solve this problem for a group of surgeon end users whose literacy
> with neuroimaging is highly variable.
> That out of the way, let me just restate the problem. I have a
> pre-operative MRI scan and a post-operative CT scan.  The post-op scan
> contains electrodes which are inserted into the brain during surgery.
> The first issue is to fuse (register) the post-operative CT to the
> pre-op MRI, to be able to visualize the relationship between
> anatomical structures--on the MRI--and electrode positions on the CT.
> The second issue is that I want to be able to transform both the MRI
> and fused CT into Talairach or MNI space, and subsequently determine
> the coordinates of the electrodes in the brain, by navigating over the
> electrodes with the mouse cursor.
> Using the "Expert Automated Registration" module--by my understanding
> a combination of a linear and a non-linear transform--I have
> consistently been able to get a good-quality registration of the
> post-op CT with the pre-op MRI. However, I do not know how to then
> transform the MRI or CT into Talairach or MNI space using Slicer,
> allow me to then navigate and determine the electrode coordinates.
> It is worth mentioning that none of the other Slicer registration
> algorithms seem to produce satisfactory co-registrations of our
> particular CT and MRI scans. I wonder if this is due to distortion of
> landmarks by electrode artifact.
> Hopefully what I'm asking is clear; any help you could provide would
> be greatly appreciated.
> Regards, and thanks again,
> Tejas Sankar, MD, FRCSC Neurosurgery
> University of Toronto
> _______________________________________________
> 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


_______________________________________________
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