Hello guys!
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?
Hi @enriquegf,
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
m20_seg_labeled_discs.nii.gz (77.7 KB) m20_seg_labeled.nii.gz (84.3 KB) m20_seg.nii.gz (4.8 KB)
I’m not sure what you did, but results look OK on my end:
| VertLevel | MEAN(area) |
|---|---|
| 8 | 44.05825885019590 |
| 7 | 48.594102619341700 |
| 6 | 53.87744611037150 |
| 5 | 63.68126638238550 |
| 4 | 57.07686534077420 |
| 3 | 57.532144223958000 |
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
Thanks!
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.