sct_testing -- Spinal Cord Toolbox (4.2.2) Will run through the following tests: - sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc - in parallel with 256 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_convert sct_compute_ernst_angle sct_compute_hausdorff_distance sct_compute_mtr sct_compute_mscc sct_compute_snr sct_concat_transfo sct_create_mask sct_crop_image sct_dice_coefficient sct_detect_pmj sct_dmri_compute_dti sct_dmri_concat_b0_and_dwi sct_dmri_concat_bvals sct_dmri_concat_bvecs sct_dmri_create_noisemask sct_dmri_compute_bvalue sct_dmri_moco sct_dmri_separate_b0_and_dwi sct_dmri_transpose_bvecs sct_extract_metric sct_flatten_sagittal sct_fmri_compute_tsnr sct_fmri_moco sct_get_centerline sct_image sct_label_utils sct_label_vertebrae sct_maths sct_merge_images sct_process_segmentation sct_propseg sct_qc sct_register_multimodal sct_register_to_template sct_resample sct_smooth_spinalcord sct_straighten_spinalcord sct_warp_template Checking sct_deepseg_gm.............................[FAIL] ==================================================================================================== sct_deepseg_gm -i t2s/t2s_uncropped.nii.gz -o output.nii.gz -qc testing-qc ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_gm.py", line 141, in run_main() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_gm.py", line 124, in run_main use_tta) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_gm/deepseg_gm.py", line 315, in segment_file use_tta) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_gm/deepseg_gm.py", line 218, in segment_volume with open(metadata_abs_path) as fp: FileNotFoundError: [Errno 2] No such file or directory: '/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/data/deepseg_gm_models/large_model.json' Checking sct_deepseg_lesion.........................[FAIL] ==================================================================================================== sct_deepseg_lesion -i t2/t2.nii.gz -c t2 ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Method: Centerline algorithm: svm Assumes brain section included in the image: True Create temporary folder (/tmp/sct-20210119195805.837341-47chpjc7)... Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_lesion.py", line 178, in main() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_lesion.py", line 154, in main brain_bool=brain_bool, remove_temp_files=remove_temp_files, verbose=verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_lesion/core.py", line 164, in deep_segmentation_MSlesion centerline_fname=file_ctr) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_sc/core.py", line 63, in find_centerline ParamCenterline(algo_fitting='optic', contrast=contrast_type)) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/core.py", line 151, in get_centerline im_centerline = optic.detect_centerline(im_seg, param.contrast, verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/optic.py", line 119, in detect_centerline sct.run(cmd_optic, is_sct_binary=True, verbose=0) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_utils.py", line 311, in run raise RunError(output) sct_utils.RunError: OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 terminate called after throwing an instance of 'cv::Exception' what(): /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp:3214: error: (-215) dsize.area() > 0 in function resize terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively Checking sct_deepseg_sc.............................[FAIL] ==================================================================================================== sct_deepseg_sc -i t2/t2.nii.gz -c t2 -igt t2/t2_seg_manual.nii.gz -qc testing-qc ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Config deepseg_sc: Centerline algorithm: svm Brain in image: True Kernel dimension: 2d Contrast: t2 Threshold: 0.7 Create temporary folder (/tmp/sct-20210119195809.417333-p9vmfyyw)... Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_sc.py", line 208, in main() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_deepseg_sc.py", line 192, in main threshold_seg=threshold, remove_temp_files=remove_temp_files, verbose=verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_sc/core.py", line 477, in deep_segmentation_spinalcord centerline_fname=file_ctr) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/deepseg_sc/core.py", line 63, in find_centerline ParamCenterline(algo_fitting='optic', contrast=contrast_type)) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/core.py", line 151, in get_centerline im_centerline = optic.detect_centerline(im_seg, param.contrast, verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/optic.py", line 119, in detect_centerline sct.run(cmd_optic, is_sct_binary=True, verbose=0) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_utils.py", line 311, in run raise RunError(output) sct_utils.RunError: OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 terminate called after throwing an instance of 'cv::Exception' terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively Checking sct_analyze_lesion.........................[OK] Checking sct_analyze_texture........................[OK] Checking sct_apply_transfo..........................[OK] Checking sct_convert................................[OK] Checking sct_compute_ernst_angle....................[OK] Checking sct_compute_hausdorff_distance.............[OK] Checking sct_compute_mtr............................[OK] Checking sct_compute_mscc...........................[OK] Checking sct_compute_snr............................[OK] Checking sct_concat_transfo.........................[OK] Checking sct_create_mask............................[OK] Checking sct_crop_image.............................[OK] Checking sct_dice_coefficient.......................[OK] Checking sct_detect_pmj.............................[FAIL] ==================================================================================================== sct_detect_pmj -i template/template/PAM50_small_t2.nii.gz -c t2 -qc testing-qc ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Create temporary folder (/tmp/sct-20210119195811.319895-revu84eh)... cp template/template/PAM50_small_t2.nii.gz /tmp/sct-20210119195811.319895-revu84eh WARNING: File PAM50_small_t2.nii.gz already exists. Will overwrite it. sct_crop_image -i PAM50_small_t2.nii.gz -zmin 35 -zmax 36 -o PAM50_small_t2_midSag.nii # in /tmp/sct-20210119195811.319895-revu84eh Run PMJ detector ['isct_spine_detect', '/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/data/pmj_models/t2_model', 'PAM50_small_t2_midSag', 'PAM50_small_t2_map_pmj'] Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_detect_pmj.py", line 323, in main() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_detect_pmj.py", line 306, in main fname_out, tmp_dir = detector.apply() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_detect_pmj.py", line 141, in apply self.detect() # run the detection File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_detect_pmj.py", line 204, in detect sct.run(cmd_pmj, verbose=0, is_sct_binary=True) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_utils.py", line 311, in run raise RunError(output) sct_utils.RunError: OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 terminate called after throwing an instance of 'cv::Exception' what(): /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp:3214: error: (-215) dsize.area() > 0 in function resize Checking sct_dmri_compute_dti.......................[OK] Checking sct_dmri_concat_b0_and_dwi.................[OK] Checking sct_dmri_concat_bvals......................[OK] Checking sct_dmri_concat_bvecs......................[OK] Checking sct_dmri_create_noisemask..................[OK] Checking sct_dmri_compute_bvalue....................[OK] Checking sct_dmri_moco..............................[OK] Checking sct_dmri_separate_b0_and_dwi...............[OK] Checking sct_dmri_transpose_bvecs...................[OK] Checking sct_extract_metric.........................[OK] Checking sct_flatten_sagittal.......................[OK] Checking sct_fmri_compute_tsnr......................[OK] Checking sct_fmri_moco..............................[OK] Checking sct_get_centerline.........................[FAIL] ==================================================================================================== sct_get_centerline -i t2s/t2s.nii.gz -c t2s ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_get_centerline.py", line 147, in run_main() File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_get_centerline.py", line 137, in run_main verbose=verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/core.py", line 151, in get_centerline im_centerline = optic.detect_centerline(im_seg, param.contrast, verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/optic.py", line 119, in detect_centerline sct.run(cmd_optic, is_sct_binary=True, verbose=0) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_utils.py", line 311, in run raise RunError(output) sct_utils.RunError: OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 terminate called after throwing an instance of 'cv::Exception' what(): /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp:3214: error: (-215) dsize.area() > 0 in function resize Checking sct_image..................................[OK] Checking sct_label_utils............................[OK] Checking sct_label_vertebrae........................[OK] Checking sct_maths..................................[OK] Checking sct_merge_images...........................[OK] Checking sct_process_segmentation...................[OK] Checking sct_propseg................................[FAIL] ==================================================================================================== sct_propseg -i t2/t2.nii.gz -c t2 -qc testing-qc ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) Folder testing-qc has been created. Create temporary folder (/tmp/sct-20210119195811.653582-label_vertebrae-nfhcnytu)... Traceback (most recent call last): File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_propseg.py", line 626, in res = main(arguments) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_propseg.py", line 610, in main img_seg = propseg(img_input, arguments) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_propseg.py", line 550, in propseg image_centerline = optic.detect_centerline(image_input, contrast_type, verbose) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/spinalcordtoolbox/centerline/optic.py", line 119, in detect_centerline sct.run(cmd_optic, is_sct_binary=True, verbose=0) File "/data/u_mkaptan_software/SpinalCord_version422/spinalcordtoolbox-4.2.2/scripts/sct_utils.py", line 311, in run raise RunError(output) sct_utils.RunError: OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 OpenCV Error: Assertion failed (dsize.area() > 0) in resize, file /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp, line 3214 terminate called after throwing an instance of 'cv::Exception' what(): /myopt/opencv/opencv-3.0.0/modules/imgproc/src/imgwarp.cpp:3214: error: (-215) dsize.area() > 0 in function resize terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively terminate called recursively Checking sct_qc.....................................[OK] Checking sct_register_multimodal....................[OK] Checking sct_register_to_template...................[OK] Checking sct_resample...............................[OK] Checking sct_smooth_spinalcord......................[OK] Checking sct_straighten_spinalcord..................[OK] Checking sct_warp_template..........................[OK] status: [1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0] Failures: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc sct_detect_pmj sct_get_centerline sct_propseg Finished! Elapsed time: 98s