I am running CSA analysis for different studies, but recently I came across with a potential issue; when I analyze some nii the majority of the CSA in the cervical spinal cord are in magnitude of 10s (ie C3 45) but with one study I am finding magnitudes of 100 (ie 900). Can someone give me some orientation of what is happening?
Thank you for reaching out. Could you please clarify what you mean by “10s (ie C3 45)”? CSA are in mm^2, so I am not sure what you meant here.
I’m also confused by “magnitudes of 100 (ie 900)”. What is the unit here? And what does “ie 900” mean?
I am sorry for this barely legible explanation. I upload both screenshot from what I ve done.
I obtained results from one study in magnitude of hundreds, but in the same patient in a previous study it is in magnitude of tens.
It is probably caused by your NIfTI headers, which are corrupted (ie: the qform/sform does not reflect the actual physical dimensions). If you upload an example image and segmentation that yields those CSAs I can have a look.
ok! here is the .nii of this patient from which I obtained this results.
Thank very very much! I am just beginning to try SCT as a neurologist m20.nii.gz (2.4 MB)
hum, the header looks good-- could you please also upload the segmentation you used to compute the CSA?
Of course! here it is
I’m not sure what you did, but results look OK on my end:
CSV output: csa.csv (2.9 KB)
I used this command (SCT v5.1.0):
sct_process_segmentation -i m20_seg.nii.gz -vertfile m20_seg_labeled.nii.gz -vert 3:8 -perlevel 1
I will re-run it to try to look for what error I might have.
If you could write the exact syntax you typed it is helpful for us to debug. Usually we ask users to copy/paste the syntax and output from the Terminal.
Hi @enriquegf, just following up to see if you still have an issue, or if we can close this ticket?