Implemented method to register lesion mask to MT space #95
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After testing image-based and segmentation-based registration, I think the segmentation-based registration is better suited and probably more robust. Example in Compare:
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Example of registered lesion:
It is far from perfect. The main issue is likely that the lesion mask comes from a sagittal image (with 3mm thick slices) to be mapped onto an axial image (with 0.9 mm in-plane resolution). Unfortunately there is nothing we can do about it. |
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@leelisae I still need to add code to exclude the lesion mask from the calculation of MTR, but could you already give the lesion registration a try? You just need to 'git checkout' that branch: Also make sure to upgrade to SCT 6.3 as indicated above. |
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@jcohenadad Yes, I upgraded to SCT 6.3 then, ran your code for an example subject - lesion registration looks good! Thank you (and also in advance for the code to calculate MTR for ROIs excluding lesions)! |
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Update: upsampling the PSIR to 0.7mm iso before running the segmentation and registration seems to improve the registration quality. See below (comparing: PSIR_resampled_reg, PSIR_reg, mt_t1):
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Comparing the new registration method (632bdab) vs. the old one :
sliiiiightly better |
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Next step: test new contrast-agnostic model |
The new code outputs CSV files with suffix '_nolesion'
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69e9183 now implements code to estimate MTR excluding lesions. See example below the left and right CST (green) that is subtracted from the registered lesion mask (yellow):
And the resulting output CSV in the whole spinal cord without the lesion mask (first row) with with the lesion mask (2nd row):
@lisaeylee can you give it a try? |
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@lisaeylee If you haven't tried it already, please make sure to update to SCT's latest branch to benefit from the latest contrast-agnostic model that works better for PSIR/STIR data (spinalcordtoolbox/spinalcordtoolbox@bb479d8) |
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@jcohenadad I had a few other tasks to complete earlier this week for a deadline, but this is on my agenda for today and tomorrow! To clarify, is this feature implemented in the SCT v6.3 that I recently updated to, or is it a separate update? If the latter, where can I find the exact steps to follow? |
Separate update. Step to follow (just do steps 1 and 3): https://spinalcordtoolbox.com/user_section/installation/mac.html#option-2-install-from-github-development |
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@jcohenadad I just realized that the update you suggested above failed to install. Here is the install_sct_log.txt. Do you know why this might be? Thank you! |
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@joshuacwnewton would you mind helping @lisaeylee with this? thanks! |
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It's possible that this is Big Sur-specific? macOS 10.16/11.0 hit "end of life" last year, and so we're not able to test it on GitHub anymore, so an issue may have slipped through (e.g. the lazy loading code). I'm setting up a virtual machine to test on Big Sur right now, though. :) |
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Aha! I was able to reproduce the issue on my Big Sur virtual machine:
This should make it much easier to debug. I'll update when I have a fix. :) |
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I've isolated the issue to
If I reinstall from I have reported this issue to the For now, I will make sure we avoid this buggy version in SCT. To quickly fix your installation, you can run this command to downgrade the version of cd $SCT_DIR
./python/envs/venv_sct/bin/pip3 install onnx==1.16.0(I've also minimized the prior debugging we did to keep this PR neat and tidy.) |
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@joshuacwnewton - I tried 1) running the command you provided above, 2) remove current spinalcordtoolbox, 3) re-install spinalcordtoolbox. But, I still get the same error message (see below). Did I misunderstand anything? What else can I try? I am very grateful for your generous help and time on this! Console logLast login: Mon Jun 17 16:58:16 on ttys005
(base) msresearch@MSs-MacBook-Pro ~ % cd $SCT_DIR
./python/envs/venv_sct/bin/pip3 install onnx==1.16.0
Collecting onnx==1.16.0
Using cached onnx-1.16.0-cp39-cp39-macosx_10_15_x86_64.whl.metadata (16 kB)
Requirement already satisfied: numpy>=1.20 in ./python/envs/venv_sct/lib/python3.9/site-packages (from onnx==1.16.0) (1.26.4)
Requirement already satisfied: protobuf>=3.20.2 in ./python/envs/venv_sct/lib/python3.9/site-packages (from onnx==1.16.0) (4.25.3)
Using cached onnx-1.16.0-cp39-cp39-macosx_10_15_x86_64.whl (15.0 MB)
Installing collected packages: onnx
Attempting uninstall: onnx
Found existing installation: onnx 1.16.1
Uninstalling onnx-1.16.1:
Successfully uninstalled onnx-1.16.1
Successfully installed onnx-1.16.0
(base) msresearch@MSs-MacBook-Pro spinalcordtoolbox % ls
CHANGES.md bin python
CODE_OF_CONDUCT.md contrib requirements.txt
CONTRIBUTING.rst data setup.cfg
LICENSE documentation setup.py
MANIFEST.in install_sct spinalcordtoolbox
README.rst install_sct.bat spinalcordtoolbox.egg-info
batch_processing.sh install_sct_log.txt testing
(base) msresearch@MSs-MacBook-Pro spinalcordtoolbox % cd ../
(base) msresearch@MSs-MacBook-Pro ~ % ls
Applications Library Public sct_testing_data
Desktop Movies canproco spinalcordtoolbox
Documents Music opt spinalcordtoolbox-6.3
Downloads Pictures sct_6.3 test
(base) msresearch@MSs-MacBook-Pro ~ % rm spinalcordtoolbox
rm: spinalcordtoolbox: is a directory
(base) msresearch@MSs-MacBook-Pro ~ % rm -r spinalcordtoolbox
override r--r--r-- msresearch/staff for spinalcordtoolbox/.git/objects/pack/pack-ad75749c08ca27b1462868679981ace0fe909904.idx? y
override r--r--r-- msresearch/staff for spinalcordtoolbox/.git/objects/pack/pack-ad75749c08ca27b1462868679981ace0fe909904.pack? y
(base) msresearch@MSs-MacBook-Pro ~ % ls
Applications Library Public sct_testing_data
Desktop Movies canproco spinalcordtoolbox-6.3
Documents Music opt test
Downloads Pictures sct_6.3
(base) msresearch@MSs-MacBook-Pro ~ % git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox
cd spinalcordtoolbox
Cloning into 'spinalcordtoolbox'...
remote: Enumerating objects: 61660, done.
remote: Counting objects: 100% (2879/2879), done.
remote: Compressing objects: 100% (1739/1739), done.
remote: Total 61660 (delta 1948), reused 1845 (delta 1117), pack-reused 58781
Receiving objects: 100% (61660/61660), 119.61 MiB | 13.79 MiB/s, done.
Resolving deltas: 100% (35603/35603), done.
(base) msresearch@MSs-MacBook-Pro spinalcordtoolbox % ./install_sct
*******************************
* Welcome to SCT installation *
*******************************
Checking OS type and version...
Darwin MSs-MacBook-Pro.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:27 PDT 2021; root:xnu-7195.141.2~5/RELEASE_ARM64_T8101 arm64
ProductVersion: 11.5.2
Checking requirements...
OK!
SCT version ......... 6.4.dev0
Installation type ... in-place
Operating system .... osx (11.5.2)
Shell config ........ /Users/msresearch/.zshrc
SCT will be installed here: [/Users/msresearch/spinalcordtoolbox]
Do you agree? [y]es/[n]o: y
Skipping copy of source files (source and destination folders are the same)
Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y
Downloading Miniconda...
curl -sS -o /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/tmp.u1bGwRsO/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
Installing Miniconda...
bash /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/tmp.u1bGwRsO/miniconda.sh -p /Users/msresearch/spinalcordtoolbox/python -b -f
PREFIX=/Users/msresearch/spinalcordtoolbox/python
Unpacking payload ...
Installing base environment...
Preparing transaction: ...working... done
Executing transaction: ...working...
done
installation finished.
Creating conda environment...
Retrieving notices: ...working... done
Channels:
- defaults
Platform: osx-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /Users/msresearch/spinalcordtoolbox/python/envs/venv_sct
added / updated specs:
- python=3.9
The following packages will be downloaded:
package | build
---------------------------|-----------------
openssl-3.0.14 | h46256e1_0 4.4 MB
pip-24.0 | py39hecd8cb5_0 2.6 MB
python-3.9.19 | h5ee71fb_1 12.7 MB
setuptools-69.5.1 | py39hecd8cb5_0 1004 KB
wheel-0.43.0 | py39hecd8cb5_0 107 KB
------------------------------------------------------------
Total: 20.8 MB
The following NEW packages will be INSTALLED:
ca-certificates pkgs/main/osx-64::ca-certificates-2024.3.11-hecd8cb5_0
libcxx pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0
libffi pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_1
ncurses pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0
openssl pkgs/main/osx-64::openssl-3.0.14-h46256e1_0
pip pkgs/main/osx-64::pip-24.0-py39hecd8cb5_0
python pkgs/main/osx-64::python-3.9.19-h5ee71fb_1
readline pkgs/main/osx-64::readline-8.2-hca72f7f_0
setuptools pkgs/main/osx-64::setuptools-69.5.1-py39hecd8cb5_0
sqlite pkgs/main/osx-64::sqlite-3.45.3-h6c40b1e_0
tk pkgs/main/osx-64::tk-8.6.14-h4d00af3_0
tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0
wheel pkgs/main/osx-64::wheel-0.43.0-py39hecd8cb5_0
xz pkgs/main/osx-64::xz-5.4.6-h6c40b1e_1
zlib pkgs/main/osx-64::zlib-1.2.13-h4b97444_1
Downloading and Extracting Packages: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
# $ conda activate /Users/msresearch/spinalcordtoolbox/python/envs/venv_sct
#
# To deactivate an active environment, use
#
# $ conda deactivate
Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (24.0)
Installing Python dependencies...
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Downloading sentry_sdk-2.6.0-py2.py3-none-any.whl (296 kB)
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Downloading setuptools-70.1.0-py3-none-any.whl (882 kB)
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Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, traitlets, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, platformdirs, pillow, packaging, ordered-set, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cython, cycler, coverage, click, charset-normalizer, certifi, bids-validator, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, transforms3d, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, matplotlib-inline, markdown-it-py, lazy-loader, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, trx-python, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, gitpython, dicom2nifti, wandb, typer, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, dipy, batchgenerators, pybids, neurite, acvl-utils, voxelmorph, torchio, nnunetv2, ivadomed
Successfully installed Deprecated-1.2.14 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.6 certifi-2024.6.2 charset-normalizer-3.3.2 click-8.1.7 coloredlogs-15.0.1 connected-components-3d-3.16.1 contourpy-1.2.1 coverage-7.5.3 csv-diff-1.1 cycler-0.12.1 cython-3.0.10 deepdiff-7.0.1 dicom2nifti-2.4.11 dictdiffer-0.9.0 dipy-1.8.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 exceptiongroup-1.2.1 filelock-3.15.1 flatbuffers-24.3.25 fonttools-4.53.0 formulaic-0.3.4 fsspec-2024.6.0 future-1.0.0 gitdb-4.0.11 gitpython-3.1.43 graphviz-0.20.3 grpcio-1.64.1 h5py-3.11.0 humanfriendly-10.0 humanize-4.9.0 idna-3.7 imagecodecs-2024.6.1 imageio-2.34.1 importlib-metadata-7.1.0 importlib-resources-6.4.0 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.10 jinja2-3.1.4 joblib-1.4.2 kiwisolver-1.4.5 lazy-loader-0.4 linecache2-1.0.0 loguru-0.7.2 lxml-5.2.2 markdown-3.6 markdown-it-py-3.0.0 matplotlib-3.9.0 matplotlib-inline-0.1.7 mdurl-0.1.2 monai-1.3.1 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-5.2.1 nilearn-0.10.4 nnunetv2-2.4.2 num2words-0.5.13 numpy-1.26.4 onnx-1.16.1 onnxruntime-1.18.0 ordered-set-4.1.0 packaging-24.1 pandas-1.5.3 pillow-10.3.0 platformdirs-4.2.2 pluggy-1.5.0 portalocker-2.8.2 protobuf-4.25.3 psutil-6.0.0 pybids-0.15.5 pydicom-2.4.4 pygments-2.18.0 pyparsing-3.1.2 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.2.2 pytest-cov-5.0.0 pytest_console_scripts-1.4.1 python-dateutil-2.9.0.post0 python-gdcm-3.0.24.1 pytz-2024.1 pyyaml-6.0.1 requests-2.32.3 requirements-parser-0.9.0 rich-13.7.1 scikit-image-0.24.0 scikit-learn-1.5.0 scipy-1.13.1 seaborn-0.13.2 sentry-sdk-2.6.0 setproctitle-1.3.3 setuptools-69.5.1 setuptools-scm-8.1.0 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12.1 tensorboard-2.17.0 tensorboard-data-server-0.7.2 threadpoolctl-3.5.0 tifffile-2024.6.18 tomli-2.0.1 torch-2.2.2 torchio-0.19.7 torchvision-0.17.2 tqdm-4.66.4 traceback2-1.4.0 traitlets-5.14.3 transforms3d-0.4.2 trx-python-0.2.9 typer-0.12.3 types-setuptools-70.0.0.20240524 typing-extensions-4.12.2 unittest2-1.1.0 urllib3-2.2.2 voxelmorph-0.2 wandb-0.17.2 werkzeug-3.0.3 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.2.0 xlwt-1.3.0 yacs-0.1.8 zipp-3.19.2
Installing spinalcordtoolbox...
Obtaining file:///Users/msresearch/spinalcordtoolbox
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Installing collected packages: spinalcordtoolbox
Running setup.py develop for spinalcordtoolbox
Successfully installed spinalcordtoolbox-6.4.dev0
Creating launchers for Python scripts...
Installing binaries...
sct_download_data -d binaries_osx -k
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d binaries_osx -k
--
Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221018/spinalcordtoolbox-binaries_osx.tar.gz
Downloading: spinalcordtoolbox-binaries_osx.tar.gz
Status: 100%|██████████| 65.3M/65.3M [00:04<00:00, 14.5MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-04_install-data_iafcabfs)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-04_install-data_iafcabfs
Copying data to: /Users/msresearch/spinalcordtoolbox/bin
Removing temporary folders...
Done!
All requirements installed!
Installing data...
mkdir -p /Users/msresearch/spinalcordtoolbox/data
sct_download_data -d PAM50
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d PAM50
--
Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip
Downloading: PAM50-r20240215.zip
Status: 100%|██████████| 104M/104M [00:07<00:00, 14.6MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-13_install-data_qhg25lfh)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-13_install-data_qhg25lfh
Copying data to: /Users/msresearch/spinalcordtoolbox/data/PAM50
Removing temporary folders...
Done!
sct_download_data -d deepseg_sc_models
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d deepseg_sc_models
--
Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip
Downloading: 20220325_deepseg_sc_models_onnx.zip
Status: 100%|██████████| 19.5M/19.5M [00:01<00:00, 15.2MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-15_install-data_hxlj1mpj)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-15_install-data_hxlj1mpj
Copying data to: /Users/msresearch/spinalcordtoolbox/data/deepseg_sc_models
Removing temporary folders...
Done!
sct_download_data -d deepseg_gm_models
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d deepseg_gm_models
--
Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip
Downloading: 20220325_deepseg_gm_models_onnx.zip
Status: 100%|██████████| 2.24M/2.24M [00:00<00:00, 14.1MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-16_install-data_cat_29ik)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-16_install-data_cat_29ik
Copying data to: /Users/msresearch/spinalcordtoolbox/data/deepseg_gm_models
Removing temporary folders...
Done!
sct_download_data -d deepseg_lesion_models
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d deepseg_lesion_models
--
Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip
Downloading: 20220325_deepseg_lesion_models_onnx.zip
Status: 100%|██████████| 5.35M/5.35M [00:00<00:00, 13.3MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-18_install-data_28dkxfl4)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-18_install-data_28dkxfl4
Copying data to: /Users/msresearch/spinalcordtoolbox/data/deepseg_lesion_models
Removing temporary folders...
Done!
sct_download_data -d deepreg_models
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d deepreg_models
--
Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip
Downloading: models.zip
Status: 100%|██████████| 158M/158M [00:09<00:00, 16.0MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-28_install-data_1w9wslk9)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-28_install-data_1w9wslk9
Copying data to: /Users/msresearch/spinalcordtoolbox/data/deepreg_models
Removing temporary folders...
Done!
sct_download_data -d PAM50_normalized_metrics
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_download_data -d PAM50_normalized_metrics
--
Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip
Downloading: PAM50-normalized-metrics-r20230222.zip
Status: 6.92MB [00:00, 8.05MB/s]
Creating temporary folder (/var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-31_install-data_0b80ly4s)
Unzip data to: /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/sct_2024-06-19_11-59-31_install-data_0b80ly4s
Copying data to: /Users/msresearch/spinalcordtoolbox/data/PAM50_normalized_metrics
Removing temporary folders...
Done!
Status: 100%|██████████| 18.0M/18.0M [00:01<00:00, 15.1MB/s]
Validate installation...
--
Spinal Cord Toolbox (git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c)
sct_check_dependencies
--
SYSTEM INFORMATION
------------------
SCT info:
- version: git-master-a631c4d978cbd1d8a5e14da4b7a30e244eca2f9c
- path: /Users/msresearch/spinalcordtoolbox
OS: osx (macOS-10.16-x86_64-i386-64bit)
CPU cores: Available: 8, Used by ITK functions: 8
RAM: Total: 8192MB, Used: 644MB, Available: 1014MB
OPTIONAL DEPENDENCIES
---------------------
Check FSLeyes version...............................[OK] (1.0.13)
MANDATORY DEPENDENCIES
----------------------
Check Python executable.............................[OK]
Using bundled python 3.9.19 (main, May 6 2024, 14:46:57)
[Clang 14.0.6 ] at /Users/msresearch/spinalcordtoolbox/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if dipy is installed........................../Users/msresearch/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_check_dependencies.py:163: UserWarning: Private repos not supported. Skipping.
for req in requirements.parse(requirements_txt):
[OK] (1.8.0)
Check if ivadomed is installed......................[OK] (2.9.10)
Check if matplotlib is installed....................[OK] (3.9.0)
Check if matplotlib-inline is installed.............[OK]
Check if monai is installed.........................
Installation validation Failed!
Installation failed!
Please find the file "/Users/msresearch/spinalcordtoolbox/install_sct_log.txt",
then upload it as a .txt attachment in a new topic on SCT's forum:
--> https://forum.spinalcordmri.org/c/sct
(base) msresearch@MSs-MacBook-Pro spinalcordtoolbox %
|
|
Ah, yes! There has been a misunderstanding. There is no need to re-run (you can rerun sct_check_dependencies after installing onnx, and it should no longer crash, indicating that the broken installation has been fixed) |
|
@joshuacwnewton - It works now! I successfully ran the full script and got results very similar, though not exactly the same, as Julien's above. The slight differences in the numbers might be due to the different SCT versions we're using. I will run the script for the rest of the subjects and do QC. Hopefully, we can submit the revised manuscript soon! Thank you and your team for your very kind help! 
|
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Yay! I'm so glad things are working now. Thank you so much for your patience, and for providing lots of useful debugging information to help narrow down the issue. |
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This PR implements the following features:
Warning
The script is now calling sct_deepseg (to segment the PSIR image), which requires SCT v6.3 or later.
TODO:
Fixes #91