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Hi, 

 

Thank you for your interest in our tool. Currently these three nuclei are not segmented by the network implementation, but they will be segmented by the Bayesian tool once we have integrated it into FreeSurfer.

 

The Pc, VM and Pt are the three smallest nuclei in our atlas, with volumes generally less than 2-3 mm^3. As such they often do not have the highest posterior probability in any voxels during Bayesian segmentation and therefore don't appear in the output segmentations or only in very few voxels. We therefore decided to remove these labels when training the network implementation. 

 

To view the segmentations you can use the following command substituting the paths for the segmentation, V1, FA and aligned T1 volumes

 

freeview <path/to/t1> <path/to/segmentation>:colormap=LUT -dti <path/to/V1> <path/to/FA>

 

Best wishes, 

Henry

 

========================================================

Henry Tregidgo, PhD

Research Associate

 

Centre for Medical Image Computing (CMIC),

University College London (UCL)

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 胡馨月 <hudunhu@gmail.com>
Sent: 18 May 2023 13:15
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

 

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Dear FreeSurfer Experts,

I hope you are doing well. I have encountered an issue while using the Thalamic NucleiDTI module in FreeSurfer and would appreciate your guidance.

I am attempting to segment the thalamus using the module, but the Pc, VM, and Pt nuclei are missing in the segmentation results. Could you please advise me on resolving this issue?

Additionally, I would like instructions on how to display the Thalamic NucleiDTI module results in Freeview. Please guide me on the steps to visualize the results accurately in Freeview.

Thank you for your support. I look forward to your response.

Best regards,

Xinyue Hu West China Hospital of Sichuan University