Error when running sct_label_vertebrae.py ,SCT 4.1.0

sahar_sabaghian · December 5, 2019, 4:14pm

automatic c2c3 detection fails in SpineGeneric pipeline and also when I perform “deepseg and sct_label_vertebrae.py” separately I got this error too.

would you please guide me to solve it?

the error is :

Run C2-C3 detector…

Traceback (most recent call last):
File “/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py”, line 40, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘data_midSlice_pred_svm.hdr’

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py”, line 427, in
main()
File “/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py”, line 330, in main
im_label_c2c3 = detect_c2c3(im_data, im_seg, contrast, verbose=verbose_detect_c2c3)
File “/home/sahar/sct_4.1.0/spinalcordtoolbox/vertebrae/detect_c2c3.py”, line 79, in detect_c2c3
pred = nib.load(‘data_midSlice_pred_svm.hdr’).get_data()
File “/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py”, line 42, in load
raise FileNotFoundError(“No such file or no access: ‘%s’” % filename)
FileNotFoundError: No such file or no access: ‘data_midSlice_pred_svm.hdr’

jcohenadad · December 5, 2019, 4:36pm

hi @sahar_sabaghian

could you please let us know the exact syntax you wrote, as well as on which image?

best,
julien

sahar_sabaghian · December 5, 2019, 5:42pm

Sure,
I can see the T1-deepseg in index.html and it is great . I just got the error in T1 labeling and then algorithm stops. I converted my own subject image to BIDS format and then used it.

sahar@sahar-Inspiron-N5110:~/Desktop/multi_subject$ sct_run_batch parameters.sh process_data.sh
Processing:
sub-tehran07 
GNU parallel is installed! ......


Successfully generated the QC results in /home/sahar/Desktop/multi_subject/results/qc/_json/qc_2019_12_05_122122.442472.json
Use the following command to see the results in a browser:
xdg-open "/home/sahar/Desktop/multi_subject/results/qc/index.html"
file_t1_seg=$FILESEG
# Create labels in the cord at C2 and C5 mid-vertebral levels (only if it does not exist)
label_if_does_not_exist ${file_t1} ${file_t1_seg}

--
Spinal Cord Toolbox (4.1.0)


Create temporary folder (/tmp/sct-20191205122141.411383-label_vertebrae-05z9d03w)...

Copying input data to tmp folder...

Straighten spinal cord...

Create temporary folder (/tmp/sct-20191205122146.499622-straighten_spinalcord-kg0wg49m)...

Copy files to tmp folder...
Window length needs to be >= 3. Returning input signal.
Window length needs to be >= 3. Returning input signal.
Fitting centerline using B-spline approximation
Error on approximation = 4.24 mm
Error on approximation = 1.08 mm
Error on approximation = 0.34 mm
Error on approximation = 0.14 mm
Error on approximation = 0.07 mm
Error on approximation = 0.05 mm
Error on approximation = 0.04 mm
Error on approximation = 0.04 mm
Error on approximation = 0.04 mm
Create the straight space and the safe zone
Length of spinal cord: 177.5476699136718
Size of spinal cord in z direction: 172.71632054933784
Ratio length/size: 1.0279727436814743
Safe zone boundaries (curved space): [-74.22210076277835, 98.49421978655948]
Safe zone boundaries (straight space): [-76.63777544494535, 100.90989446872648]
Pad input volume to account for spinal cord length...
Time to generate centerline: 287.0 ms
100%|██████████| 179/179 [00:41<00:00,  4.36it/s]
100%|██████████| 328/328 [13:09<00:00,  2.41s/it]Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/sahar/sct_4.1.0/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n 'BSpline[3]' # in /tmp/sct-20191205122146.499622-straighten_spinalcord-kg0wg49m
Generate output files...
  File created: ./warp_curve2straight.nii.gz
  File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20191205122146.499622-straighten_spinalcord-kg0wg49m/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
sct_convert -i /tmp/sct-20191205122146.499622-straighten_spinalcord-kg0wg49m/tmp.anat_rigid_warp.nii.gz -o ./data_straight.nii
  File created: ./data_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20191205122146.499622-straighten_spinalcord-kg0wg49m

Finished! Elapsed time: 966 s

Resample to 0.5mm isotropic...
sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20191205122141.411383-label_vertebrae-05z9d03w

Apply straightening to segmentation...
/home/sahar/sct_4.1.0/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20191205122141.411383-label_vertebrae-05z9d03w
sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20191205122141.411383-label_vertebrae-05z9d03w

Create label to identify disc...
Creating temporary folder...
Run C2-C3 detector...

Traceback (most recent call last):
  File "/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'data_midSlice_pred_svm.hdr'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 427, in <module>
    main()
  File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 330, in main
    im_label_c2c3 = detect_c2c3(im_data, im_seg, contrast, verbose=verbose_detect_c2c3)
  File "/home/sahar/sct_4.1.0/spinalcordtoolbox/vertebrae/detect_c2c3.py", line 79, in detect_c2c3
    pred = nib.load('data_midSlice_pred_svm.hdr').get_data()
  File "/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
    raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: 'data_midSlice_pred_svm.hdr'

FINISHED

sahar_sabaghian · December 5, 2019, 5:54pm

I found also this text in “detect_c2c3.py” file. my error happens exactly in these lines.

 # The command below will fail, but we don't care because it will output an image (prediction), which we
    # will use later on.
    s, o = sct.run(cmd_detection, verbose=0, is_sct_binary=True, raise_exception=False)
    **pred = nib.load('data_midSlice_pred_svm.hdr').get_data()**
    if verbose >= 2:
        # copy the "prediction data before post-processing" in an Image object
        nii_pred_before_postPro = nii_midSlice.copy()
        nii_pred_before_postPro.data = pred  # 2D data with orientation, mid sag slice of the original data
        nii_pred_before_postPro.save("pred_midSlice_before_postPro.nii.gz")  # save it)
    # DEBUG trick: check if the detection succeed by running: fsleyes data_midSlice data_midSlice_pred_svm -cm red -dr 0 100
    # If a "red cluster" is observed in the neighbourhood of C2C3, then the model detected it.

jcohenadad · December 5, 2019, 6:18pm

@sahar_sabaghian there might be something wrong with the segmentation on sub-tehran07, that leads to issues with the vertebral labeling. Could you please share your T1w and T1w_seg, which you used as an input to sct_label_vertebrae?

sahar_sabaghian · December 5, 2019, 7:36pm

I test it with another subject from neuroopen dataset (sub-amu-04), but i got the same error again.

jcohenadad · December 5, 2019, 7:52pm

can you run the following and let me know if you encounter an error (if you did, please copy/paste the entire terminal output):

sct_download_data -d sct_example_data
cd sct_example_data/t1/
sct_deepseg_sc -i t1.nii.gz -c t1 -qc qc
sct_label_vertebrae -i t1.nii.gz -s t1_seg.nii.gz -c t1 -qc qc

sahar_sabaghian · December 5, 2019, 8:26pm

the same error.

sahar@sahar-Inspiron-N5110:~$ sct_download_data -d sct_example_data

--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/kjcgs/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kjcgs/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kjcgs/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kjcgs/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /kjcgs/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20180525_sct_example_data.zip
Downloading 20180525_sct_example_data.zip...
Status: 44.3MB [00:55, 798kB/s]                                                 

Create temporary folder (/tmp/sct-20191205145445.685533-66t9k5on)...

Unzip data to: /tmp/sct-20191205145445.685533-66t9k5on

Check if folder already exists on the destination path...

Remove temporary folders...
Done!

sahar@sahar-Inspiron-N5110:~$ cd sct_example_data/t1/
sahar@sahar-Inspiron-N5110:~/sct_example_data/t1$ sct_deepseg_sc -i t1.nii.gz -c t1 -qc qc

--
Spinal Cord Toolbox (4.1.0)

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t1
  Threshold: 0.15

Create temporary folder (/tmp/sct-20191205145635.363025-u9pf5629)...
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
Remove temporary files...
rm -rf /tmp/sct-20191205150048.220558-xrwnjars
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...
Binarizing the resampled segmentation...
Removing small objects above slice #174
Removing small objects above slice #174
Compute shape analysis: 100%|###############| 175/175 [00:06<00:00, 25.39iter/s]
Found isolated voxels on slice 0, Removing them
Remove temporary files...
rm -rf /tmp/sct-20191205145635.363025-u9pf5629

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm
QcImage: layout with Axial slice
Compute center of mass at each slice
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/css/style.css /home/sahar/sct_example_data/t1/qc/_assets/css
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/main.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/js/animation.js /home/sahar/sct_example_data/t1/qc/_assets/js
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /home/sahar/sct_example_data/t1/qc/_assets/imgs
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /home/sahar/sct_example_data/t1/qc/_assets/imgs
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /home/sahar/sct_example_data/t1/qc/_assets/imgs
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /home/sahar/sct_example_data/t1/qc/_assets/fonts
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /home/sahar/sct_example_data/t1/qc/_assets/fonts
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /home/sahar/sct_example_data/t1/qc/_assets/fonts
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /home/sahar/sct_example_data/t1/qc/_assets/fonts
cp /home/sahar/sct_4.1.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /home/sahar/sct_example_data/t1/qc/_assets/fonts
Successfully generated the QC results in /home/sahar/sct_example_data/t1/qc/_json/qc_2019_12_05_150530.389396.json
Use the following command to see the results in a browser:
xdg-open "/home/sahar/sct_example_data/t1/qc/index.html"
sahar@sahar-Inspiron-N5110:~/sct_example_data/t1$ xdg-open "/home/sahar/sct_example_data/t1/qc/index.html"
sahar@sahar-Inspiron-N5110:~/sct_example_data/t1$ sct_label_vertebrae -i t1.nii.gz -s t1_seg.nii.gz -c t1 -qc qc

--
Spinal Cord Toolbox (4.1.0)

Folder qc has been created.

Create temporary folder (/tmp/sct-20191205150730.774082-label_vertebrae-vhfqpcrp)...

Copying input data to tmp folder...

Straighten spinal cord...

Create temporary folder (/tmp/sct-20191205150735.890279-straighten_spinalcord-0qfjp4hn)...

Copy files to tmp folder...
Window length needs to be >= 3. Returning input signal.
Window length needs to be >= 3. Returning input signal.
Fitting centerline using B-spline approximation
Error on approximation = 0.43 mm
Error on approximation = 0.3 mm
Error on approximation = 0.24 mm
Error on approximation = 0.07 mm
Error on approximation = 0.06 mm
Error on approximation = 0.03 mm
Error on approximation = 0.03 mm
Error on approximation = 0.03 mm
Create the straight space and the safe zone
Length of spinal cord: 176.64136791379283
Size of spinal cord in z direction: 173.18351500618556
Ratio length/size: 1.0199664090862446
Safe zone boundaries (curved space): [-107.36721871141057, 65.81629629477499]
Safe zone boundaries (straight space): [-109.09614516521421, 67.54522274857862]
Pad input volume to account for spinal cord length...
Time to generate centerline: 319.0 ms
100%|█████████████████████████████████████████| 178/178 [00:43<00:00,  4.13it/s]
100%|█████████████████████████████████████████| 326/326 [13:32<00:00,  2.49s/it]
Warping field generated: tmp.curve2straight.nii.gz
Warping field generated: tmp.straight2curve.nii.gz
Apply transformation to input image...
/home/sahar/sct_4.1.0/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n 'BSpline[3]' # in /tmp/sct-20191205150735.890279-straighten_spinalcord-0qfjp4hn
Generate output files...
  File created: ./warp_curve2straight.nii.gz
  File created: ./warp_straight2curve.nii.gz
cp /tmp/sct-20191205150735.890279-straighten_spinalcord-0qfjp4hn/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
sct_convert -i /tmp/sct-20191205150735.890279-straighten_spinalcord-0qfjp4hn/tmp.anat_rigid_warp.nii.gz -o ./data_straight.nii
  File created: ./data_straight.nii
Remove temporary files...
rm -rf /tmp/sct-20191205150735.890279-straighten_spinalcord-0qfjp4hn

Finished! Elapsed time: 977 s

Resample to 0.5mm isotropic...
sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20191205150730.774082-label_vertebrae-vhfqpcrp

Apply straightening to segmentation...
/home/sahar/sct_4.1.0/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20191205150730.774082-label_vertebrae-vhfqpcrp
sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20191205150730.774082-label_vertebrae-vhfqpcrp

Create label to identify disc...
Creating temporary folder...
Run C2-C3 detector...
Traceback (most recent call last):
  File "/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load
    stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'data_midSlice_pred_svm.hdr'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 427, in <module>
    main()
  File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 330, in main
    im_label_c2c3 = detect_c2c3(im_data, im_seg, contrast, verbose=verbose_detect_c2c3)
  File "/home/sahar/sct_4.1.0/spinalcordtoolbox/vertebrae/detect_c2c3.py", line 79, in detect_c2c3
    pred = nib.load('data_midSlice_pred_svm.hdr').get_data()
  File "/home/sahar/.local/lib/python3.6/site-packages/nibabel/loadsave.py", line 42, in load
    raise FileNotFoundError("No such file or no access: '%s'" % filename)
FileNotFoundError: No such file or no access: 'data_midSlice_pred_svm.hdr'

jcohenadad · December 5, 2019, 8:42pm

hum, this is strange. Before digging further, could you please run the following and send us the output:

sct_check_dependencies
sct_testing

sahar_sabaghian · December 5, 2019, 9:15pm

ok, I will send the result. I have another question. would you please tell me how the ‘data_midSlice_pred_svm.hdr’ is obtained within the algorithm, I mean where is its location because the error is " no such file or access".

pred = nib.load(‘data_midSlice_pred_svm.hdr’).get_data()
[/quote]

thanks

jcohenadad · December 5, 2019, 9:24pm

@sahar_sabaghian the problem could be related to a faulty installation of SCT on your end. Which is why I am asking you to run the commands above.

sahar_sabaghian · December 5, 2019, 9:24pm

Testing shows that “Checking sct_label_vertebrae…[FAIL]” , but i do not actually know where is the problem to solve. could you please tell me. thanks

sahar@sahar-Inspiron-N5110:~$ sct_check_dependencies

--
Spinal Cord Toolbox (4.1.0)

SCT info:
- version: 4.1.0
- path: /home/sahar/sct_4.1.0
OS: linux (Linux-4.4.0-21-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 8, Used by SCT: 8
RAM: MemTotal:        6014016 kB
total        used        free      shared  buff/cache   available
Mem:           5873         817        4144         243         910        4741
Swap:             0           0           0
Check Python executable.............................[OK]
  Using bundled python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) 
[GCC 7.3.0] at /home/sahar/sct_4.1.0/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.17.4)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.0.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras is installed.........................[OK] (2.3.1)
Check if matplotlib is installed....................[OK] (3.1.2)
Check if nibabel is installed.......................[OK] (2.5.1)
Check if pandas is installed........................[OK] (0.25.3)
Check if psutil is installed........................[OK] (5.6.7)
Check if pyqt5 is installed.........................[OK]
Check if pytest is installed........................[OK] (5.3.1)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.3)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.22)
Check if tensorflow is installed....................[OK] (2.0.0)
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.40.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.7)
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]

sahar@sahar-Inspiron-N5110:~$ sct_testing

--
Spinal Cord Toolbox (4.1.0)

Will run through the following tests:
- sequentially: sct_deepseg_gm sct_deepseg_lesion sct_deepseg_sc
- in parallel with 8 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.............................[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_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.............................[OK]
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.........................[OK]
Checking sct_image..................................[OK]
Checking sct_label_utils............................[OK]
Checking sct_label_vertebrae........................[FAIL]
   
   ====================================================================================================
   sct_label_vertebrae -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -c t2 -initfile t2/init_label_vertebrae.txt -t template -qc testing-qc
   ====================================================================================================
   
   
   --
   Spinal Cord Toolbox (4.1.0)
   
   Folder testing-qc has been created.
   
   Create temporary folder (/tmp/sct-20191205161218.557424-label_vertebrae-bv13l0t3)...
   
   Copying input data to tmp folder...
   
   Straighten spinal cord...
   Reusing existing warping field which seems to be valid
   cp /home/sahar/sct_testing_data/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
   cp /home/sahar/sct_testing_data/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
   cp /home/sahar/sct_testing_data/straight_ref.nii.gz straight_ref.nii.gz
   sct_apply_transfo -i data.nii -w warp_curve2straight.nii.gz -d straight_ref.nii.gz -o data_straight.nii # in /tmp/sct-20191205161218.557424-label_vertebrae-bv13l0t3
   Traceback (most recent call last):
   File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 427, in <module>
   main()
   File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 254, in main
   s, o = sct.run(['sct_apply_transfo', '-i', 'data.nii', '-w', 'warp_curve2straight.nii.gz', '-d', 'straight_ref.nii.gz', '-o', 'data_straight.nii'])
   File "/home/sahar/sct_4.1.0/scripts/sct_utils.py", line 311, in run
   raise RunError(output)
   sct_utils.RunError:
   --
   Spinal Cord Toolbox (4.1.0)
   
   
   Parse list of warping fields...
   Error: make sure warp_curve2straight.nii.gz is an image.
   Traceback (most recent call last):
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 356, in <module>
   main()
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 346, in main
   transform.apply()
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 165, in apply
   and Image(list_warp[idx_warp]).header.get_intent()[0] != 'vector':
   File "/home/sahar/sct_4.1.0/spinalcordtoolbox/image.py", line 243, in __init__
   self.loadFromPath(param, verbose)
   File "/home/sahar/sct_4.1.0/spinalcordtoolbox/image.py", line 347, in loadFromPath
   self.data = self.im_file.get_data()
   AttributeError: 'NoneType' object has no attribute 'get_data'
   
   ====================================================================================================
   sct_label_vertebrae -i t2/t2.nii.gz -s t2/t2_seg.nii.gz -c t2 -discfile t2/labels.nii.gz
   ====================================================================================================
   
   
   --
   Spinal Cord Toolbox (4.1.0)
   
   
   Create temporary folder (/tmp/sct-20191205161226.045613-label_vertebrae-y_2unfu3)...
   
   Copying input data to tmp folder...
   
   Straighten spinal cord...
   Reusing existing warping field which seems to be valid
   cp /home/sahar/sct_testing_data/warp_curve2straight.nii.gz warp_curve2straight.nii.gz
   cp /home/sahar/sct_testing_data/warp_straight2curve.nii.gz warp_straight2curve.nii.gz
   cp /home/sahar/sct_testing_data/straight_ref.nii.gz straight_ref.nii.gz
   sct_apply_transfo -i data.nii -w warp_curve2straight.nii.gz -d straight_ref.nii.gz -o data_straight.nii # in /tmp/sct-20191205161226.045613-label_vertebrae-y_2unfu3
   Traceback (most recent call last):
   File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 427, in <module>
   main()
   File "/home/sahar/sct_4.1.0/scripts/sct_label_vertebrae.py", line 254, in main
   s, o = sct.run(['sct_apply_transfo', '-i', 'data.nii', '-w', 'warp_curve2straight.nii.gz', '-d', 'straight_ref.nii.gz', '-o', 'data_straight.nii'])
   File "/home/sahar/sct_4.1.0/scripts/sct_utils.py", line 311, in run
   raise RunError(output)
   sct_utils.RunError:
   --
   Spinal Cord Toolbox (4.1.0)
   
   
   Parse list of warping fields...
   Error: make sure warp_curve2straight.nii.gz is an image.
   Traceback (most recent call last):
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 356, in <module>
   main()
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 346, in main
   transform.apply()
   File "/home/sahar/sct_4.1.0/scripts/sct_apply_transfo.py", line 165, in apply
   and Image(list_warp[idx_warp]).header.get_intent()[0] != 'vector':
   File "/home/sahar/sct_4.1.0/spinalcordtoolbox/image.py", line 243, in __init__
   self.loadFromPath(param, verbose)
   File "/home/sahar/sct_4.1.0/spinalcordtoolbox/image.py", line 347, in loadFromPath
   self.data = self.im_file.get_data()
   AttributeError: 'NoneType' object has no attribute 'get_data'
Checking sct_maths..................................[OK]
Checking sct_merge_images...........................[OK]
Checking sct_process_segmentation...................[OK]
Checking sct_propseg................................[OK]
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: [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, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
Failures: sct_label_vertebrae
Finished! Elapsed time: 247s

jcohenadad · December 5, 2019, 9:27pm

Your installation of SCT likely had some issues. Could you please re-run the installation, and copy/paste the entire output so I can understand why the installation failed.

sahar_sabaghian · December 5, 2019, 9:52pm

I did it but unfortunately it has an error. due to the limitation of body characters I sent the text in two parts.

sahar@sahar-Inspiron-N5110:~$ cd /home/sahar/spinalcordtoolbox-4.1.0
sahar@sahar-Inspiron-N5110:~/spinalcordtoolbox-4.1.0$ ./install_sct


*******************************
* Welcome to SCT installation *
*******************************



Checking requirements...


SCT version ......... 4.1.0
Installation type ... package
Operating system .... linux
Shell config ........ /home/sahar/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: y

--> Crash reports will be sent to the SCT development team. Thank you!


SCT will be installed here: [/home/sahar/sct_4.1.0]

Do you agree? [y]es/[n]o: y

Copying source files from /home/sahar/spinalcordtoolbox-4.1.0 to /home/sahar/sct_4.1.0

.......................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...


rm -rf /home/sahar/sct_4.1.0/python


mkdir -p /home/sahar/sct_4.1.0/python


wget -O /tmp/tmp.4weYR1ve4C/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2019-12-05 16:35:10--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.201.79, 104.18.200.79, 2606:4700::6812:c84f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.201.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: ‘/tmp/tmp.4weYR1ve4C/miniconda.sh’

/tmp/tmp.4weYR1ve4C 100%[===================>]  68.46M   862KB/s    in 76s     

2019-12-05 16:36:27 (919 KB/s) - ‘/tmp/tmp.4weYR1ve4C/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.4weYR1ve4C/miniconda.sh -p /home/sahar/sct_4.1.0/python -b -f

PREFIX=/home/sahar/sct_4.1.0/python
Unpacking payload ...
Extracting : pycosat-0.6.3-py37h14c3975_0.conda:   3%| | 1/35 [00:00<00:04,  7.4Extracting : idna-2.8-py37_0.conda:   6%|▍       | 2/35 [00:00<00:04,  7.48it/s]Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:  11%| | 4/35 [00:00<00:04,  7.48iExtracting : libgcc-ng-9.1.0-hdf63c60_0.conda:  14%|▏| 5/35 [00:00<00:03,  9.74iExtracting : six-1.12.0-py37_0.conda:  14%|▊     | 5/35 [00:00<00:03,  9.74it/s]Extracting : libffi-3.2.1-hd88cf55_4.conda:  17%|▏| 6/35 [00:00<00:02,  9.74it/sExtracting : ncurses-6.1-he6710b0_1.conda:  20%|▏| 7/35 [00:00<00:02,  9.74it/s]Extracting : ruamel_yaml-0.15.46-py37h14c3975_0.conda:  23%|▏| 8/35 [00:00<00:02Extracting : yaml-0.1.7-had09818_2.conda:  26%|▌ | 9/35 [00:00<00:02,  9.74it/s]Extracting : _libgcc_mutex-0.1-main.conda:  29%|▎| 10/35 [00:00<00:02,  9.74it/sExtracting : pycparser-2.19-py37_0.conda:  31%|▎| 11/35 [00:00<00:02,  9.74it/s]Extracting : libedit-3.1.20181209-hc058e9b_0.conda:  34%|▎| 12/35 [00:00<00:02, Extracting : pyopenssl-19.0.0-py37_0.conda:  37%|▎| 13/35 [00:00<00:02,  9.74it/Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  40%|▍| 14/35 [0Extracting : urllib3-1.24.2-py37_0.conda:  43%|▍| 15/35 [00:00<00:02,  9.74it/s]Extracting : python-3.7.4-h265db76_1.conda:  49%|▍| 17/35 [00:00<00:01, 12.71it/Extracting : chardet-3.0.4-py37_1003.conda:  51%|▌| 18/35 [00:00<00:01, 12.71it/Extracting : chardet-3.0.4-py37_1003.conda:  54%|▌| 19/35 [00:00<00:01, 10.82it/Extracting : zlib-1.2.11-h7b6447c_3.conda:  54%|▌| 19/35 [00:00<00:01, 10.82it/sExtracting : requests-2.22.0-py37_0.conda:  57%|▌| 20/35 [00:00<00:01, 10.82it/sExtracting : readline-7.0-h7b6447c_5.conda:  60%|▌| 21/35 [00:00<00:01, 10.82it/Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  63%|▋| 22/35 [00:00<00:01, 10Extracting : pip-19.3.1-py37_0.tar.bz2:  66%|█▉ | 23/35 [00:00<00:01, 10.82it/s]Extracting : pysocks-1.7.1-py37_0.tar.bz2:  69%|▋| 24/35 [00:00<00:01, 10.82it/sExtracting : conda-4.7.12-py37_0.tar.bz2:  71%|▋| 25/35 [00:01<00:00, 10.82it/s]Extracting : ca-certificates-2019.10.16-0.tar.bz2:  74%|▋| 26/35 [00:01<00:00, 1Extracting : asn1crypto-1.2.0-py37_0.tar.bz2:  77%|▊| 27/35 [00:01<00:00, 13.89iExtracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  80%|▊| 28/35 [00:01<00:00Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2:  83%|▊| 29/35 [00:01<00:00, 13.89Extracting : cffi-1.13.0-py37h2e261b9_0.tar.bz2:  86%|▊| 30/35 [00:01<00:00, 13.Extracting : setuptools-41.4.0-py37_0.tar.bz2:  89%|▉| 31/35 [00:01<00:00, 13.89Extracting : openssl-1.1.1d-h7b6447c_3.tar.bz2:  91%|▉| 32/35 [00:01<00:00, 13.8Extracting : openssl-1.1.1d-h7b6447c_3.tar.bz2:  94%|▉| 33/35 [00:01<00:00, 17.7Extracting : wheel-0.33.6-py37_0.tar.bz2:  94%|▉| 33/35 [00:01<00:00, 17.77it/s]Extracting : certifi-2019.9.11-py37_0.tar.bz2:  97%|▉| 34/35 [00:01<00:00, 17.77                                                                                Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/sahar/sct_4.1.0/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/sahar/sct_4.1.0/python/envs/venv_sct

  added / updated specs:
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.11.27 |                0         132 KB
    certifi-2019.11.28         |           py36_0         156 KB
    pip-19.3.1                 |           py36_0         1.9 MB
    python-3.6.9               |       h265db76_0        30.2 MB
    setuptools-42.0.2          |           py36_0         653 KB
    sqlite-3.30.1              |       h7b6447c_0         1.9 MB
    wheel-0.33.6               |           py36_0          40 KB
    ------------------------------------------------------------
                                           Total:        35.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.11.27-0
  certifi            pkgs/main/linux-64::certifi-2019.11.28-py36_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py36_0
  python             pkgs/main/linux-64::python-3.6.9-h265db76_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-42.0.2-py36_0
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  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Proceed ([y]/n)? 

Downloading and Extracting Packages
pip-19.3.1           | 1.9 MB    | ##################################### | 100% 
wheel-0.33.6         | 40 KB     | ##################################### | 100% 
setuptools-42.0.2    | 653 KB    | ##################################### | 100% 
certifi-2019.11.28   | 156 KB    | ##################################### | 100% 
python-3.6.9         | 30.2 MB   | ##################################### | 100% 
ca-certificates-2019 | 132 KB    | ##################################### | 100% 
sqlite-3.30.1        | 1.9 MB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate


Installing Python dependencies...

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Installing collected packages: numpy
Successfully installed numpy-1.17.4
Ignoring tensorflow: markers 'platform_system == "Darwin" and "15." in platform_release' don't match your environment
Requirement already satisfied: numpy in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.17.4)
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Collecting nibabel
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Collecting pytest-cov
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Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests->-r requirements.txt (line 15)) (2019.11.28)
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Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorflow->-r requirements.txt (line 19)) (0.33.6)
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  Using cached https://files.pythonhosted.org/packages/05/57/ce2e7a8fa7c0afb54a0581b14a65b56e62b5759dbc98e80627142b8a3704/oauthlib-3.1.0-py2.py3-none-any.whl
Installing collected packages: pycparser, cffi, six, cryptography, nibabel, h5py, scipy, dipy, futures, pyyaml, keras-applications, keras-preprocessing, Keras, kiwisolver, python-dateutil, cycler, pyparsing, matplotlib, pytz, pandas, psutil, PyQt5-sip, pyqt5, more-itertools, zipp, importlib-metadata, pluggy, py, packaging, attrs, wcwidth, pytest, coverage, pytest-cov, raven, chardet, pyOpenSSL, idna, urllib3, requests, pillow, imageio, decorator, networkx, PyWavelets, scikit-image, joblib, scikit-learn, protobuf, absl-py, pyasn1, pyasn1-modules, cachetools, rsa, google-auth, markdown, oauthlib, requests-oauthlib, google-auth-oauthlib, grpcio, werkzeug, tensorboard, wrapt, gast, astor, opt-einsum, termcolor, tensorflow-estimator, google-pasta, tensorflow, xlrd, xlwt, xlutils, tqdm, transforms3d
Successfully installed Keras-2.3.1 PyQt5-sip-12.7.0 PyWavelets-1.1.1 absl-py-0.8.1 astor-0.8.0 attrs-19.3.0 cachetools-3.1.1 cffi-1.13.2 chardet-3.0.4 coverage-4.5.4 cryptography-2.8 cycler-0.10.0 decorator-4.4.1 dipy-1.0.0 futures-3.1.1 gast-0.2.2 google-auth-1.7.1 google-auth-oauthlib-0.4.1 google-pasta-0.1.8 grpcio-1.25.0 h5py-2.10.0 idna-2.8 imageio-2.6.1 importlib-metadata-1.2.0 joblib-0.14.0 keras-applications-1.0.8 keras-preprocessing-1.1.0 kiwisolver-1.1.0 markdown-3.1.1 matplotlib-3.1.2 more-itertools-8.0.0 networkx-2.4 nibabel-2.5.1 oauthlib-3.1.0 opt-einsum-3.1.0 packaging-19.2 pandas-0.25.3 pillow-6.2.1 pluggy-0.13.1 protobuf-3.11.1 psutil-5.6.7 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pycparser-2.19 pyparsing-2.4.5 pyqt5-5.13.2 pytest-5.3.1 pytest-cov-2.8.1 python-dateutil-2.8.1 pytz-2019.3 pyyaml-5.2 raven-6.10.0 requests-2.22.0 requests-oauthlib-1.3.0 rsa-4.0 scikit-image-0.16.2 scikit-learn-0.22 scipy-1.3.3 six-1.13.0 tensorboard-2.0.2 tensorflow-2.0.0 tensorflow-estimator-2.0.1 termcolor-1.1.0 tqdm-4.40.0 transforms3d-0.3.1 urllib3-1.25.7 wcwidth-0.1.7 werkzeug-0.16.0 wrapt-1.11.2 xlrd-1.2.0 xlutils-2.0.0 xlwt-1.3.0 zipp-0.6.0
Obtaining file:///home/sahar/sct_4.1.0
Installing collected packages: spinalcordtoolbox
  Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox

Creating launchers for Python scripts...


Make shell scripts executable...


Creating symbolic links for Shell scripts...

sahar_sabaghian · December 5, 2019, 9:53pm


Installing binaries...


sct_download_data -d binaries_debian -o /home/sahar/sct_4.1.0/bin


--
Spinal Cord Toolbox (4.1.0)

Folder /home/sahar/sct_4.1.0/bin has been created.

Trying URL: https://osf.io/bt58d/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /bt58d/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /bt58d/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /bt58d/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /bt58d/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20190930_sct_binaries_linux.tar.gz
Downloading 20190930_sct_binaries_linux.tar.gz...
Status: 81.1MB [01:35, 848kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164103.654628-jx1fq50m)...

Unzip data to: /tmp/sct-20191205164103.654628-jx1fq50m

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


All requirements installed!


. /home/sahar/sct_4.1.0/python/bin/activate /home/sahar/sct_4.1.0/python


Installing data...


rm -rf /home/sahar/sct_4.1.0/data


mkdir -p /home/sahar/sct_4.1.0/data


cd /home/sahar/sct_4.1.0/data


sct_download_data -d PAM50


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/kc3jx/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kc3jx/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kc3jx/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /kc3jx/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /kc3jx/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20181214_PAM50.zip
Downloading 20181214_pam50.zip...
Status: 70.8MB [01:23, 850kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164239.062522-z87c0bmy)...

Unzip data to: /tmp/sct-20191205164239.062522-z87c0bmy

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d gm_model


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/ugscu/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /ugscu/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /ugscu/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /ugscu/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /ugscu/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20160922_gm_model.zip
Downloading 20160922_gm_model.zip...
Status: 10.3MB [00:11, 871kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164256.597817-rpc3d28n)...

Unzip data to: /tmp/sct-20191205164256.597817-rpc3d28n

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d optic_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/g4fwn/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /g4fwn/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /g4fwn/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /g4fwn/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /g4fwn/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20170413_optic_models.zip
Downloading 20170413_optic_models.zip...
Status: 17.7kB [00:00, 99.5kB/s]                                                

Create temporary folder (/tmp/sct-20191205164302.272191-7lp6fxyc)...

Unzip data to: /tmp/sct-20191205164302.272191-7lp6fxyc

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d pmj_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/4gufr/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /4gufr/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /4gufr/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /4gufr/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /4gufr/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20170922_pmj_models.zip
Downloading 20170922_pmj_models.zip...
Status: 8.87kB [00:00, 5.76MB/s]                                                

Create temporary folder (/tmp/sct-20191205164307.496233-acti4m2b)...

Unzip data to: /tmp/sct-20191205164307.496233-acti4m2b

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_sc_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/avf97/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /avf97/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /avf97/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /avf97/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /avf97/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20180610_deepseg_sc_models.zip
Downloading 20180610_deepseg_sc_models.zip...
Status: 58.7MB [01:05, 891kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164418.712245-qlqx9fef)...

Unzip data to: /tmp/sct-20191205164418.712245-qlqx9fef

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_gm_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/b9y4x/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /b9y4x/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /b9y4x/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /b9y4x/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /b9y4x/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20180205_deepseg_gm_models.zip
Downloading 20180205_deepseg_gm_models.zip...
Status: 2.28MB [00:04, 466kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164429.557469-y_fbpoyn)...

Unzip data to: /tmp/sct-20191205164429.557469-y_fbpoyn

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d deepseg_lesion_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/eg7v9/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /eg7v9/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /eg7v9/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /eg7v9/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /eg7v9/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20180613_deepseg_lesion_models.zip
Downloading 20180613_deepseg_lesion_models.zip...
Status: 16.0MB [00:18, 889kB/s]                                                 

Create temporary folder (/tmp/sct-20191205164452.818718-d24ff_sw)...

Unzip data to: /tmp/sct-20191205164452.818718-d24ff_sw

Check if folder already exists on the destination path...

Remove temporary folders...
Done!


sct_download_data -d c2c3_disc_models


--
Spinal Cord Toolbox (4.1.0)


Trying URL: https://osf.io/t97ap/?action=download
Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /t97ap/?action=download
Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /t97ap/?action=download
Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)': /t97ap/?action=download
Link download error, trying next mirror (error was: HTTPSConnectionPool(host='osf.io', port=443): Max retries exceeded with url: /t97ap/?action=download (Caused by SSLError(SSLError("bad handshake: SysCallError(-1, 'Unexpected EOF')",),)))

Trying URL: https://www.neuro.polymtl.ca/_media/downloads/sct/20190117_c2c3_disc_models.zip
Unexpected: link doesn't provide a filename

Download error

Create temporary folder (/tmp/sct-20191205164458.404496-mb2hgxpz)...

Unzip data to: /tmp/sct-20191205164458.404496-mb2hgxpz
Traceback (most recent call last):
  File "/home/sahar/sct_4.1.0/scripts/sct_download_data.py", line 248, in <module>
    res = main()
  File "/home/sahar/sct_4.1.0/scripts/sct_download_data.py", line 140, in main
    unzip(tmp_file, dest_tmp_folder, verbose)
  File "/home/sahar/sct_4.1.0/scripts/sct_download_data.py", line 174, in unzip
    if compressed.endswith('zip'):
AttributeError: 'NoneType' object has no attribute 'endswith'

ERROR: Command failed.


Installation failed

sahar@sahar-Inspiron-N5110:~/spinalcordtoolbox-4.1.0$

jcohenadad · December 5, 2019, 10:13pm

The 2nd mirror for the zip file c2c3_disc_models was not uploaded (our mistake). I’ve now uploaded it, can you please try again?

sahar_sabaghian · December 5, 2019, 10:38pm

Thank you. great, it works. just let me test “sct_run_batch parameters.sh process_data.sh” and then I will tell you the results.

sahar_sabaghian · December 6, 2019, 6:59pm

All worked properly.
Thank you for taking the time and answering my questions patiently.