Slicer Help

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Slicer Help

gabriele pasqua
Dear all,

I'm new in 3dSlicer, I hope you will help me.

I want to compute FA, MD indexes from DTI image of spinal cord.

I'm using 4.5.0 version.

I'm able to process DWI image and estimate DTI, but i want to register a T2 image with DTI in order to define the ROIs.

How can i do it?

For DTI processing, I'm using this pipeline:

- DWI converter 

- Joint Rician Filtering of DWI

- DWI to DTI estimation;

- DTI scalar measurements

Is it correct?

Thank you so much for your help

Best regards,

Gabriele

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Re: Slicer Help

Sonia Pujol
Dear Gabriela,

The pipeline you are using is correct. To align the T2 volume with the DTI dataset, you may co-register the T2 volume to the baseline image using the General Registration (BRAINS) module.

Below is a link to the Slicer 4.5 Image registration tutorial and the Slicer Registration Case Library (RegLib C03).

Best Regards,

Sonia




On 29 Jun 2016, at 06:19 am, gabriele pasqua <[hidden email]> wrote:

Dear all,

I'm new in 3dSlicer, I hope you will help me.

I want to compute FA, MD indexes from DTI image of spinal cord.

I'm using 4.5.0 version.

I'm able to process DWI image and estimate DTI, but i want to register a T2 image with DTI in order to define the ROIs.

How can i do it?

For DTI processing, I'm using this pipeline:

- DWI converter 

- Joint Rician Filtering of DWI

- DWI to DTI estimation;

- DTI scalar measurements

Is it correct?

Thank you so much for your help

Best regards,

Gabriele
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----
Sonia Pujol, Ph.D.
Surgical Planning Laboratory
Brigham and Women’s Hospital, Harvard Medical School
Boston, MA 02115


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slicer help

gabriele pasqua
In reply to this post by gabriele pasqua

Hi, I am Gabriel

I am trying to register a T2 image with DTI in order to define the ROIs, in order to compute FA, MD indexes from DTI image of spinal cord.

I have T2 and DTI images.

I am using this pipeline you sent me by email, but it doesn’t work ( it gives me errors) :

1.     Compute Registration: open the General Registration (BRAINS) module

1.    Input Images: Fixed Image Volume: T2

2.    Input Images: Moving Image Volume: DTI_baseline

3.    Output Settings:

1.  Slicer BSpline Transform (create new transform, rename to: "Xf1_DTbase-T2_BSpline")

2.  Slicer Linear Transform none

3.  Output Image Volume (create new volume, rename to: "DTIbaseline_Xf1"

4.    Registration Phases: select/check Rigid , Rigid+Scale, Affine, BSpline

5.    Main Parameters:

1.  increase Percentage of Samples to 0.006

2.  set B-Spline Grid Size to 7,7,5 (we have lower resolution in the IS-direction (z), hence we set a smaller (5) grid size there)

6.    Leave all other settings at default

7.    click: Apply; runtime < 1 min.

2.     Resample DTI: We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.

1.    Open the Resample DTI Volume module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)

1.  Input Volume: select DTI

2.  Output Volume: select create new Diffusion Tensor Volume,and rename it to DTI_Xf1

3.  Reference Volume: select T2

4.  Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for Deformation Field: none ; check the displacement checkbox

5.  Leave all other settings at defaults

6.  Click Apply; runtime ~ 2 min.

2.    set T2 as background and new DTI_Xf1 volume as foreground

3.    fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.

 

How can I do? Can you please help me?

 

Best regards

Gabriele Pasqua


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Re: slicer help

inorton
Hi Gabriele,

Please open the Error Log (red-white "X" in a circle at the bottom-right of the Slicer window) and send the errors listed for the module (there may be many other informational entries, so scroll to the bottom of the Window for the latest messages).

Best,
Isaiah

On Wed, Jul 6, 2016 at 11:16 AM, gabriele pasqua <[hidden email]> wrote:

Hi, I am Gabriel

I am trying to register a T2 image with DTI in order to define the ROIs, in order to compute FA, MD indexes from DTI image of spinal cord.

I have T2 and DTI images.

I am using this pipeline you sent me by email, but it doesn’t work ( it gives me errors) :

1.     Compute Registration: open the General Registration (BRAINS) module

1.    Input Images: Fixed Image Volume: T2

2.    Input Images: Moving Image Volume: DTI_baseline

3.    Output Settings:

1.  Slicer BSpline Transform (create new transform, rename to: "Xf1_DTbase-T2_BSpline")

2.  Slicer Linear Transform none

3.  Output Image Volume (create new volume, rename to: "DTIbaseline_Xf1"

4.    Registration Phases: select/check Rigid , Rigid+Scale, Affine, BSpline

5.    Main Parameters:

1.  increase Percentage of Samples to 0.006

2.  set B-Spline Grid Size to 7,7,5 (we have lower resolution in the IS-direction (z), hence we set a smaller (5) grid size there)

6.    Leave all other settings at default

7.    click: Apply; runtime < 1 min.

2.     Resample DTI: We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.

1.    Open the Resample DTI Volume module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)

1.  Input Volume: select DTI

2.  Output Volume: select create new Diffusion Tensor Volume,and rename it to DTI_Xf1

3.  Reference Volume: select T2

4.  Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for Deformation Field: none ; check the displacement checkbox

5.  Leave all other settings at defaults

6.  Click Apply; runtime ~ 2 min.

2.    set T2 as background and new DTI_Xf1 volume as foreground

3.    fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.

 

How can I do? Can you please help me?

 

Best regards

Gabriele Pasqua


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ