Dear SCT Team:
When I was doing gray matter segmentation, the results I got were not ideal.The command I used is as follows：“sct_deepseg_gm -i t2s.nii.gz -qc ~/qc_singleSubj”.
And this is the Sample data:
Sample_Data.zip (9.4 MB)
Hi @jie_Liu,
The problem is caused by the image, which does not show the gray matter:
It is not possible for an algorithm to automatically segment something that is not visible in the image. The same goes for segmentation done by a human. I suggest updating the imaging parameters to improve the WM/GM contrast.
Cheers,
Julien
Okay, I understand, thank you very much for your reply.
Hi Julien and SCT team,
I hope it is okay, if I ask a follow-up question to this topic.
I am currently working on segmenting the spinal cord in a dataset of 80 participants, but I am encountering challenges with unsatisfactory segmentation results. Similarly, I suspect these issues may be related to suboptimal contrast between GM, WM, and CSF in the images. Unfortunately, I only have part of the cervical cord, so I hope to get the most out of the data.
Would you have any recommendations on how to enhance the contrast between these structures, either through imaging adjustments or post-processing techniques? I have attached an example of a QC report for your reference.
Kind regard,
Frederik
Hi Frederik,
A couple of things you can do:
- smooth along z (improves CNR, but problematic if strong curvature and thick slices). Example (assuming axial orientation):
sct_maths -i IMAGE -smooth 0,0,3 - smooth along the spinal cord centerline (better, but prone to interpolation error). Example:
sct_smooth_spinalcord -i IMAGE -s SEG - Try the most recent GM segmentation method that @nlaines is currently working on (you could send us 1-2 representative dataset and we can test it on your data)
Hi Julien,
Thank you very much for the reply and suggestions—I truly appreciate it!
It would be a great help if you could review the data. Unfortunately, I’m only permitted to share one example of a healthy control dataset. I’ve been allowed to send the scans of Francesco Grussu, who is helping me with the project. He sends his regards and asks you to take good care of his protons.
Would that work for you?
Have a wonderful weekend!
Kind regards,
Frederik
Sure thing! Say hi back to Francesco 
Hi Julien,
I have shared the data from a onedrive folder but I get a error message, that the invitation is rejected. Do you have any preferred ways that I can share the data safely with you?
Thank you very much for taking the time!
Kind regards,
Frederik
No preferred way. Whatever works for you (eg dropbox, gdrive with password-protected zip)