Co-registration

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Co-registration

gabriele pasqua

Hi, I'm Gabriel

 

I’m using version 4.5.0-1 and I would like to coregister T2 MRI with DTI of spinal cord, in order to extract FA values in some specific tracts.

 

I used General Registration, taking  T2 as fixed image and baseline as moving image (following instructions on wiki).

 

I got the image attached, but from this image (coregistered with FA) I cannot identify the anatomical areas I’m interested in.

 

I wouldn’t like to have a new image as result of general registration, but the two images (t2 and FA) coregistered, so that I can identify the anatomical regions on T2 and then make the ROI on FA.

 

How can I do this? Why the output image of the registration process looks like the one attached?

 

Another simply question: how can I link the different images using the visualization buttons or functions?

 

If you prefer, I can send you the dicom, so that you can check it

 

Thank you so much

 

With kind regards,

 


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Re: Co-registration

inorton
the two images (t2 and FA) coregistered, so that I can identify the anatomical regions on T2 and then make the ROI on FA.

I would suggest to use the "Diffusion Tensor Scalar Measurements" module [1] to extract the FA volume, and then place that volume under the *Output* transform from the BrainsFit registration of Baseline->T2, using the Transforms module.

Another simply question: how can I link the different images using the visualization buttons or functions?

You can link the viewers by clicking the "chain" icon (hopefully shows up as [2]) in each slice view.


[2] Inline image 1


On Wed, Jul 27, 2016 at 9:34 AM, gabriele pasqua <[hidden email]> wrote:

Hi, I'm Gabriel

 

I’m using version 4.5.0-1 and I would like to coregister T2 MRI with DTI of spinal cord, in order to extract FA values in some specific tracts.

 

I used General Registration, taking  T2 as fixed image and baseline as moving image (following instructions on wiki).

 

I got the image attached, but from this image (coregistered with FA) I cannot identify the anatomical areas I’m interested in.

 

I wouldn’t like to have a new image as result of general registration, but the two images (t2 and FA) coregistered, so that I can identify the anatomical regions on T2 and then make the ROI on FA.

 

How can I do this? Why the output image of the registration process looks like the one attached?

 

Another simply question: how can I link the different images using the visualization buttons or functions?

 

If you prefer, I can send you the dicom, so that you can check it

 

Thank you so much

 

With kind regards,

 


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co-registration

gabriele pasqua
In reply to this post by gabriele pasqua
Hi,
I’m using version 4.5.0-1 and I would like to coregister T2 MRI with DTI of spinal cord, in order to extract FA values in some specific tracts.

In order to make the Volume Masking, I have two questions:
the first one:

I would like to ask why in your tutorial the Omega threshold Parameter starts from 100 value, instead mine starts from 0.
I attached also a screenshot of my page with the mask.

 the second one:
in your tutorial with a Threshold parameter of 100 your mask is full in the cerebral area, instead mine results fractionated, as you can see in the picture attached.
How can I have a mask like yours? Why does my software has values different from the tutorial?

best regards

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