-- Spinal Cord Toolbox (version: 3.2.3) Running /mnt/algo/sct_3.2.3/scripts/sct_propseg.py -i /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/MR_frame_0001.nii.gz -c t2 -CSF -ofolder /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/ -v 1 Folder /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/ has been created. Detecting the spinal cord using OptiC cp /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/MR_frame_0001.nii.gz /tmp/sct-210606114613-y13ekz cp MR_frame_0001_centerline_optic.nii.gz /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/ rm -rf /tmp/sct-210606114613-y13ekz isct_propseg -t t2 -o /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/ -verbose -CSF -i /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/MR_frame_0001.nii.gz -init-centerline /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/MR_frame_0001_centerline_optic.nii.gz -centerline-binary # in /mnt/algo/sct_3.2.3/bin Initialization - using given centerline Total propagation length = 24.8324 mm Initial deformation : 90 points and 150 triangles Report from vnl optimizer for deformation : vnl_conjugate_gradient: 73 iterations, 1090 evaluations. Cost function reported error0.390119/0.38884 . Final step size = 0 Distance from initial mesh [mm] = 0.000345006 Propagation step 1/200 Propagation length [mm] : 8 / 800 Contrast = 8.49612 Iteration Position = ( 4.09237, -108.57, -385.982 ) Mesh deformation : 60 points and 90 triangles Report from vnl optimizer for deformation : vnl_conjugate_gradient: 21 iterations, 404 evaluations. Cost function reported error0.14485/0.144344 . Final step size = 0 Distance from initial mesh [mm] = 0.000227879 Number of bad orientation = 0 / 1 Contrast : 136.165 / 50 Distance of segmentation [mm] = 14.0003 Propagation step 2/200 Propagation length [mm] : 14.0003 / 800 Contrast = 9.73643 Iteration Position = ( 3.94304, -108.503, -391.98 ) Mesh deformation : 60 points and 90 triangles Report from vnl optimizer for deformation : vnl_conjugate_gradient: 3 iterations, 63 evaluations. Cost function reported error0.36431/0.36356 . Final step size = 0 Distance from initial mesh [mm] = 0.000123728 Number of bad orientation = 0 / 2 Contrast : 72.7442 / 50 Distance of segmentation [mm] = 20.0005 Propagation step 3/200 Propagation length [mm] : 20.0005 / 800 Contrast = 8.93023 Iteration Position = ( 3.79333, -108.465, -397.978 ) Number of bad orientation = 0 / 3 Contrast : 9.05426 / 50 Distance of segmentation [mm] = 20.0005 Initial deformation : 90 points and 150 triangles Report from vnl optimizer for deformation : vnl_conjugate_gradient: 6 iterations, 71 evaluations. Cost function reported error0.812036/0.808914 . Final step size = 0 Distance from initial mesh [mm] = 0.000664803 Propagation step 1/200 Propagation length [mm] : 7.99995 / 800 Contrast = 9.17829 Iteration Position = ( 4.49092, -108.864, -369.99 ) Number of bad orientation = 0 / 1 Contrast : 9.13695 / 50 Distance of segmentation [mm] = 7.99995 Global deformation after subdivision... 870 points and 1680 triangles Most promising points mean distance [mm] = 0.289286 Most promising points absolute mean distance [mm] = 3 Report from vnl optimizer for deformation : vnl_conjugate_gradient: 200 iterations, 2091 evaluations. Cost function reported error1.15824e+06/1.0466e+06 . Final step size = 0 Distance from initial mesh [mm] = 1.68565 Most promising points mean distance [mm] = 0.632143 Most promising points absolute mean distance [mm] = 3 Report from vnl optimizer for deformation : vnl_conjugate_gradient: 66 iterations, 737 evaluations. Cost function reported error8.66515e+06/8.61432e+06 . Final step size = 0 Distance from initial mesh [mm] = 3.0863 Distance from last mesh [mm] = 1.45204 Most promising points mean distance [mm] = 0.989286 Most promising points absolute mean distance [mm] = 3 Report from vnl optimizer for deformation : vnl_conjugate_gradient: 39 iterations, 332 evaluations. Cost function reported error1.01869e+06/978103 . Final step size = 0 Distance from initial mesh [mm] = 3.80889 Distance from last mesh [mm] = 0.776381 Most promising points mean distance [mm] = 1.01071 Most promising points absolute mean distance [mm] = 3 Distance of segmentation [mm] = 24.9961 Total propagation length = 24.9961 mm Segmentation finished. To view results, type: fslview /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/MR_frame_0001.nii.gz /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/MR_frame_0001_seg.nii.gz & Check consistency of segmentation... Create temporary folder (/tmp/sct-210606114640-propseg-BMsPdn)... tmp.segmentation.nii.gz Create temporary folder (/tmp/sct-210606114640-bHY7QF)... rm -rf /tmp/sct-210606114640-bHY7QF tmp.centerline.nii.gz Create temporary folder (/tmp/sct-210606114640-t768B6)... rm -rf /tmp/sct-210606114640-t768B6 Get data dimensions... tmp.segmentation_RPI_c.nii.gz Create temporary folder (/tmp/sct-210606114641-pLWjqe)... rm -rf /tmp/sct-210606114641-pLWjqe rm -rf /tmp/sct-210606114640-propseg-BMsPdn Copy header input --> output(s) to make sure qform is the same. WARNING: File /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/MR_frame_0001_seg.nii.gz already exists. Deleting it. WARNING: File /home/sradonjic/ROSH-10008886_WHOLE_SPINE_IMAGES/SEGMENTATION_PROPSEG/MR_frame_0001_centerline.nii.gz already exists. Deleting it. Total processing time: 0 min 29 s