Using this issue to summarize a discussion with Benjamin.
The objectives are to extract:
Ventro-dorsal diameter (AP diameter) of the spinal cord
Right-left diameter of the spinal cord
Spinal cord area
WM area
GM area
These steps require the use of SCT (these were done on v6.1):
To do so, use the following steps on the predicted file file_pred.nii.gz:
Divide the image in two files, one for GM and one for WM:
For WM : sct_maths -i ~/file_pred.nii.gz -bin 1 -o ~/file_pred_WM.nii.gz
For GM : sct_maths -i ~/file_pred.nii.gz -sub ~/file_pred_WM.nii.gz -o ~/file_pred_GM.nii.gzsct_maths -i ~/file_pred_GM.nii.gz -sub ~/file_pred_WM.nii.gz -o ~/file_pred_GM.nii.gz (need to do it twice because WM value is 2)
To obtain a Spinal cord segmentation (both WM and GM voxel are equal to 1):
sct_maths -i ~/file_pred.nii.gz -bin 0.5 -o ~/file_pred_sc.nii.gz
To measure AP and RL diameters (for each slice):
sct_process_segmentation -i ~/file_pred_sc.nii.gz -o ~/output_diameters.csv -perslice 1
The information is stored in column MEAN(diameter_AP) and MEAN(diameter_RL)
To measure SC area (for each slice):
sct_process_segmentation -i ~/file_pred_sc.nii.gz -o ~/output_sc_area.csv -perslice 1
The information is stored in MEAN(area)
To measure WM area (for each slice):
sct_process_segmentation -i ~/file_pred_WM.nii.gz -o ~/output_wm_area.csv -perslice 1
The information is stored in MEAN(area)
To measure GM area (for each slice):
sct_process_segmentation -i ~/file_pred_GM.nii.gz -o ~/output_gm_area.csv -perslice 1
The information is stored in MEAN(area)
Furthermore, it is recommanded to do apply sct_proces_segmentation on the original image and not the straightened one, as straightening might bias the results.
Using this issue to summarize a discussion with Benjamin.
The objectives are to extract:
These steps require the use of SCT (these were done on v6.1):
To do so, use the following steps on the predicted file
file_pred.nii.gz:Divide the image in two files, one for GM and one for WM: For WM :
sct_maths -i ~/file_pred.nii.gz -bin 1 -o ~/file_pred_WM.nii.gzFor GM :sct_maths -i ~/file_pred.nii.gz -sub ~/file_pred_WM.nii.gz -o ~/file_pred_GM.nii.gzsct_maths -i ~/file_pred_GM.nii.gz -sub ~/file_pred_WM.nii.gz -o ~/file_pred_GM.nii.gz(need to do it twice because WM value is 2)To obtain a Spinal cord segmentation (both WM and GM voxel are equal to 1):
sct_maths -i ~/file_pred.nii.gz -bin 0.5 -o ~/file_pred_sc.nii.gzTo measure AP and RL diameters (for each slice):
sct_process_segmentation -i ~/file_pred_sc.nii.gz -o ~/output_diameters.csv -perslice 1The information is stored in column MEAN(diameter_AP) and MEAN(diameter_RL)To measure SC area (for each slice):
sct_process_segmentation -i ~/file_pred_sc.nii.gz -o ~/output_sc_area.csv -perslice 1The information is stored in MEAN(area)To measure WM area (for each slice):
sct_process_segmentation -i ~/file_pred_WM.nii.gz -o ~/output_wm_area.csv -perslice 1The information is stored in MEAN(area)To measure GM area (for each slice):
sct_process_segmentation -i ~/file_pred_GM.nii.gz -o ~/output_gm_area.csv -perslice 1The information is stored in MEAN(area)Furthermore, it is recommanded to do apply
sct_proces_segmentationon the original image and not the straightened one, as straightening might bias the results.