Centerline for each volume

SCT
1

Hello
I am trying to get the centerline for each volume from fMRI data. my data has 230 volumes.
I use sct_get_centerline but I encountered an error.
can anyone help me with this?
Thank you
M.MA

2

Hi Mahdi. Could you please share the full terminal output (including the command you ran and the error message) that happens when you run sct_get_centerline?

Also, in your reply on this forum, you can use ~~~ at the start and end of the terminal output to format the output nicely:

~~~
like this
~~~

Thanks!

3

Hi
my error was this:

(base) mahdi@mpluss:~/Desktop/second case$ sct_get_centerline -i SP_S05_D1_RND.nii -c t2s

--
Spinal Cord Toolbox (4.3)

Traceback (most recent call last):
  File "/home/mahdi/sct_4.3/scripts/sct_get_centerline.py", line 153, in <module>
    run_main()
  File "/home/mahdi/sct_4.3/scripts/sct_get_centerline.py", line 143, in run_main
    verbose=verbose)
  File "/home/mahdi/sct_4.3/spinalcordtoolbox/centerline/core.py", line 151, in get_centerline
    im_centerline = optic.detect_centerline(im_seg, param.contrast, verbose)
  File "/home/mahdi/sct_4.3/spinalcordtoolbox/centerline/optic.py", line 119, in detect_centerline
    sct.run(cmd_optic, is_sct_binary=True, verbose=0)
  File "/home/mahdi/sct_4.3/scripts/sct_utils.py", line 310, in run
    raise RunError(output)
sct_utils.RunError: OpenCV Error: Assertion failed (_img.dims() <= 2) in minMaxLoc, file /myopt/opencv/opencv-3.0.0/modules/core/src/stat.cpp, line 2338
terminate called after throwing an instance of 'cv::Exception'
what():  /myopt/opencv/opencv-3.0.0/modules/core/src/stat.cpp:2338: error: (-215) _img.dims() <= 2 in function minMaxLoc

but I found the problem, this command just use in one volume.
thank you.

1 Like
4

Thank you for sharing an update! Iā€™m glad to hear your issue is resolved. :slightly_smiling_face: