Dear Julien
In the folder Oxford_error, there should be two subfolders.
In T2, there is a saggital T2 scan. On this scan, i can get the labeling to work without issues. Similarly, on a MEDIC scan, the procedure works.
In MTW, there is the MT weighted scan …_MTw_OLSfit_TEzero.nii, and two segmentations, from deepseg and propseg respectively. Using either of these segmentations, the labeling fails.
Datatypes are as follows:
MTw folder:
…_MTw_OLSfit_TEzero.nii: float32
…_MTw_OLSfit_TEzero_seg_deepseg: double64
…_MTw_OLSfit_TEzero_seg_propseg: double64
T2_sag folder:
sF3T_2013_40_586-152527-00001-00064-1.nii: UINT16
sF3T_2013_40_586-152527-00001-00064-1_seg.nii: double64
For sct_check_dependencies, everything is OK, as is it for sct_testing. See below.
Thank you for your help!
Daniel
SCT info:
OS: osx (Darwin-18.5.0-x86_64-i386-64bit)
CPU cores: Available: 4, Used by SCT: 4
RAM: Primary memory available: 16.00 gigabytes
Check Python executable…[OK]
Using bundled python 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:43:17)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)] at /Users/dpapp/sct_4.0.0-beta.2/python/bin/python
Check if data are installed…[OK]
Check if xlwt (1.0.0) is installed…[OK]
Check if xlutils (1.7.1) is installed…[OK]
Check if cryptography (1.6) is installed…[OK]
Check if scikit-learn (0.17.1) is installed…[OK]
Check if scikit-image (0.12.3) is installed…[OK]
Check if pyqt (4.11.4) is installed…[OK]
Check if psutil (5.2.2) is installed…[OK]
Check if matplotlib (1.5.1) is installed…[OK]
Check if pip (9.0.1) is installed…[OK]
Check if requests (2.12.4) is installed…[OK]
Check if xlrd (0.9.4) is installed…[OK]
Check if pandas (0.18.1) is installed…[OK]
Check if dipy (0.11.0) is installed…[OK]
Check if tqdm (4.11.2) is installed…[OK]
Check if nibabel (2.1.0) is installed…[OK]
Check if Keras (2.0.6) is installed…[OK]
Check if futures (3.2.0) is installed…[OK]
Check if pytest-cov (2.5.1) is installed…[OK]
Check if pytest (3.5.0) is installed…[OK]
Check if nipy (0.4.1) is installed…[OK]
Check if h5py (2.7.0) is installed…[OK]
Check if tensorflow (1.3.0) is installed…[OK]
Check if raven (6.2.1) is installed…[OK]
Check if numpy is installed (1.11.2)…[OK]
Check if scipy is installed (0.18.1)…[OK]
Check if spinalcordtoolbox is installed…[OK]
Check ANTs compatibility with OS …[OK]
Check PropSeg compatibility with OS …[OK]
Check if figure can be opened…[OK]
Total processing time: 0 min 16 s
And for sct_testing:
Will run through the following tests:
-
sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
-
in parallel with 4 jobs: sct_analyze_lesion sct_analyze_texture sct_apply_transfo sct_warp_template sct_resample sct_convert sct_image sct_maths sct_merge_images 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_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_label_utils sct_process_segmentation sct_propseg sct_register_multimodal sct_straighten_spinalcord sct_register_to_template sct_segment_graymatter sct_smooth_spinalcord sct_label_vertebrae
Checking sct_deepseg_gm…[OK]
Checking sct_deepseg_lesion…[OK]
Checking sct_deepseg_sc…[OK]
Checking sct_analyze_lesion…[OK]
Checking sct_analyze_texture…[OK]
Checking sct_apply_transfo…[OK]
Checking sct_warp_template…[OK]
Checking sct_resample…[OK]
Checking sct_convert…[OK]
Checking sct_image…[OK]
Checking sct_maths…[OK]
Checking sct_merge_images…[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…[OK]
Checking sct_dmri_compute_dti…[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…[OK]
Checking sct_label_utils…[OK]
Checking sct_process_segmentation…[OK]
Checking sct_propseg…[OK]
Checking sct_register_multimodal…[OK]
Checking sct_straighten_spinalcord…[OK]
Checking sct_register_to_template…[OK]
Checking sct_segment_graymatter…[OK]
Checking sct_smooth_spinalcord…[OK]
Checking sct_label_vertebrae…[OK]
status: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Finished! Elapsed time: 274s
Total processing time: 4 min 35 s
