MRI segmentation

[Federico Balzarotti]

Greetings,

I'm seeking assistance with a task involving MRIs provided in DICOM format. These MRIs consist of separate series for sagittal, axial, and coronal views. Unfortunately, I'm encountering difficulty opening only the three correct views simultaneously, as the reconstructed views are included but are of low quality, making segmentation impossible.

Is there a method to open all three series while synchronizing the correct views without including the reconstructed ones? I can provide a screenshot for additional context. Thank you.

[mfk16]

Here's something I do sometimes:

Be sure that the instance of itk-snap is synced to all other instances of itk-snap:

Tools --> Preferences --> sync views:

(zoom/pan if you choose)

Quit itk-snap, then restart, and drag/drop your SAG image, and expand the sagittal window:

Start another instance of itk-snap and drag/drop your AX image, and expand the AX window

Start another instance of itk-snap and drag/drop your COR image, and expand the COR window

You now have 3 instances of itk-snap, each displaying a single window.

Now when you click in one window/instance, all of the other windows/instances will sync.

Note, that if you segment in one window, the segmentation will NOT display in the other windows, and the segmentation will have the voxel size of the defining window. So, while you won't be able to import the SAG segmentation into an AX image, you can import the AX image into the instance of itk-snap that's displaying the SAG image (and SAG segmentation) and the SAG segmentation will be overlaid on the AX image.

-Matt

[Federico Balzarotti]

Thanks a lot, I will try now. Do you, by chance, know how to use the snake adaptive contour to segment healthy bone and tumor together? If I segment the vertebra then I cannot segment the tumor and vice versa. Also, maybe due to bad image resolution of the CTs they provided me, I cannot seem to be able to use the clustering function.

On 22 Mar 2024, at 01:33, mfk16 <matthe...@gmail.com> wrote:

Here's something I do sometimes:

Be sure that the instance of itk-snap is synced to all other instances of itk-snap:

Tools --> Preferences --> sync views:

<Sync.jpg>

(zoom/pan if you choose)

Quit itk-snap, then restart, and drag/drop your SAG image, and expand the sagittal window:

<SAG.jpg>

Start another instance of itk-snap and drag/drop your AX image, and expand the AX window

Start another instance of itk-snap and drag/drop your COR image, and expand the COR window

You now have 3 instances of itk-snap, each displaying a single window.

Now when you click in one window/instance, all of the other windows/instances will sync.

Note, that if you segment in one window, the segmentation will NOT display in the other windows, and the segmentation will have the voxel size of the defining window. So, while you won't be able to import the SAG segmentation into an AX image, you can import the AX image into the instance of itk-snap that's displaying the SAG image (and SAG segmentation) and the SAG segmentation will be overlaid on the AX image.

-Matt

On Wednesday, March 13, 2024 at 9:56:08 AM UTC-4 Federico Balzarotti wrote:

Greetings,

I'm seeking assistance with a task involving MRIs provided in DICOM format. These MRIs consist of separate series for sagittal, axial, and coronal views. Unfortunately, I'm encountering difficulty opening only the three correct views simultaneously, as the reconstructed views are included but are of low quality, making segmentation impossible.

Is there a method to open all three series while synchronizing the correct views without including the reconstructed ones? I can provide a screenshot for additional context. Thank you.

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<SAG.jpg>

<Sync.jpg>