Issue with C2-C5 volume

SCT
1

Hello, I want to calculate C2-C5 volumes and evaluate atrophy using the spinal cord toolbox with clinical MRIs of my MS patients. Most of the clinical MRIs I have are 1.5 tesla and there is almost no 3D MRI. There are T2 sagittal and T2 axial slices. I tried to do it separately with both, but the results are wrong with both.

I will write the codes I use in order; 1) For segmentation; sct_deepseg spinalcord -i 110_MS_Beyin-Servikal_Ta_7.nii.gz -qc /Users/cansu/qc_singleSubj

  1. For labeling; sct_label_vertebrae -i 110_MS_Brain-Cervical_Ta_7.nii.gz -s 110_MS_Brain-Cervical_Ta_7_seg.nii.gz -c t2 -qc ~/qc_singleSubj

  2. For C2-C5 volume;

sct_process_segmentation -i 110_MS_Brain-Cervical_Ta_7.nii.gz -vert 2:5 -vertfile 110_MS_Brain-Cervical_Ta_7_seg.nii.gz -o volume_c2c5.csv

When I ask the AI, after these codes, I need to obtain the mean and length from the excel output I get and multiply the two to obtain the volume result, but the results I get are very large numbers, what am I doing wrong? How can I calculate the C2-C5 volume?

2

Hi,

Thank you for reaching out.

Is 110_MS_Brain-Cervical_Ta_7.nii.gz your axial or sagittal scan? I recommend you use the sagittal scan for vertebral labeling. It will be more robust. Also, please check our latest vertebral labeling method totalspineseg, which is more robust than the current sct_label_vertebrae.

Finally, I don’t recommend to compute the “volume”, which is highly dependent on the size of the vertebrae (which is not a robust surrogate for spinal cord length), but rather the average cross-sectional area within your region of interest (in this case, C2-C5). This is what you indicated in your third command, so to avoid any confusion I suggest you rename “volume_c2c5.csv” as “csa_c2c5.csv”. If you want to compute the volume, you can simply add the CSA across the desired slices, but again I don’t recommend that. Instead, you can compute an average CSA (per slice, per levels, or across levels, as you prefer).

Best,
Julien

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