sct_testing -- Spinal Cord Toolbox (4.2.2) Trying URL: https://osf.io/yutrj/?action=download Downloading 20191031_sct_testing_data.zip... Status: 100%|###################################################################################################################################| 6.78M/6.78M [00:00<00:00, 18.1MB/s] Create temporary folder (/tmp/sct-20210118171532.701382-w_7b88vn)... Unzip data to: /tmp/sct-20210118171532.701382-w_7b88vn Check if folder already exists on the destination path... Remove temporary folders... Done! Will run through the following tests: - sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc - in parallel with 32 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) Checking sct_deepseg_lesion.........................[FAIL] ==================================================================================================== sct_deepseg_lesion -i t2/t2.nii.gz -c t2 ==================================================================================================== -- Spinal Cord Toolbox (4.2.2) 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) 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-20210118171557.935875-ydf6esc1)... cp template/template/PAM50_small_t2.nii.gz /tmp/sct-20210118171557.935875-ydf6esc1 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-20210118171557.935875-ydf6esc1 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' terminate called recursively 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' terminate called recursively terminate called recursively 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) Create temporary folder (/tmp/sct-20210118171617.536156-label_vertebrae-ud_kkze8)... 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 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_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: 409s