Problem of the segmentation

SCT
1

Dear Prof Jcohenadad

I am sorry to disturb you, but owning to my research of the DTI of the spine, I must figure out every detail of the sct.

That you write a script for me. and I have a problem about one sentence.

 # Create labels, assuming that the mid-FOV is centered at C6 vertebral level

 # sct_label_utils -i ${file_dwi_seg}.nii.gz -create-seg -1,6 -o label_C6.nii.gz

  sct_label_utils -i ${file_dwi_seg}.nii.gz -create-seg -1,6 -o label_C6.nii.gz

What is the meaning of the -create-seg-?

If you have time, looking forward to your reply.

Best Wishes

2

Hi,
-create-seg -1,6 creates a label centered in the spinal cord segmentation (in the axial plane), and centered in the middle of the FOV (in the superior inferior direction), with the value « 6 ». You can get more information from the help by typing: sct_label_utils

3

Dear Jcohenadad .
thank you for your reply,
by the way,If there is script could Initialize using slice number and vertebrae (C3) value?
I have a file of 6 slices , I just want to calculate the FA of each slice , could you give me a guidance?

Best Wishes

4

by the way,If there is script could Initialize using slice number and vertebrae (C3) value?

What process would you like to initialize?

I have a file of 6 slices , I just want to calculate the FA of each slice , could you give me a guidance?

To compute FA for each slice, you can simply run sct_extract_metric with the flag -perslice 1. Everything is explained in the latest SCT course.

Best
Julien

5

Dear Jcohenadad
Thank you very much. when I deal with the imaging, sometimes it showed content below, then the value of slice 0,1,2,3 is empty. do you think I could continue to calculate the FA of such imaging?
Split destination segmentation…
Estimate cord angle for each slice: 0%| | 0/6 [00:00<?, ?iter/s]WARNING: Slice #0 is empty. It will be ignored.
WARNING: Slice #1 is empty. It will be ignored.
WARNING: Slice #2 is empty. It will be ignored.
Estimate cord angle for each slice: 100%|███████████████████████████| 6/6 [00:00<00:00, 77.49iter/s]
Build 3D deformation field: 100%|███████████████████████████████████| 3/3 [00:00<00:00, 89.51iter/s]
Best Wishes

1 Like
6

@DKCH_HKU this issue has nothing to do with segmentation problem (which is the title of the thread). If you have another issue, please open a new ticket with a specific title. Thanks.