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Furen 2025-08-26 02:17:50 +00:00
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "1ef8063e-95e6-445f-b6b9-709cb1b568a4",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"# conda environments:\n",
"#\n",
"base /opt/conda\n",
"\n"
]
}
],
"source": [
"!/opt/conda/condabin/conda env list"
]
},
{
"cell_type": "markdown",
"id": "85145aa3-5361-47fe-a1d0-c7e1ea67cb86",
"metadata": {},
"source": [
"Install pytorch"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "2f8da521-3430-48a3-bf9e-8ec72080cb1e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Channels:\n",
" - pytorch\n",
" - nvidia\n",
" - defaults\n",
"Platform: linux-64\n",
"Collecting package metadata (repodata.json): ...working... done\n",
"Solving environment: ...working... done\n",
"\n",
"## Package Plan ##\n",
"\n",
" environment location: /home/xfr/.conda/envs/myenv\n",
"\n",
" added / updated specs:\n",
" - pytorch-cuda=12.4\n",
" - pytorch==2.5.1\n",
" - torchaudio==2.5.1\n",
" - torchvision==0.20.1\n",
"\n",
"\n",
"The following NEW packages will be INSTALLED:\n",
"\n",
" _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main \n",
" _openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu \n",
" aom pkgs/main/linux-64::aom-3.6.0-h6a678d5_0 \n",
" blas pkgs/main/linux-64::blas-1.0-mkl \n",
" brotlicffi pkgs/main/linux-64::brotlicffi-1.0.9.2-py312h6a678d5_1 \n",
" bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_6 \n",
" ca-certificates pkgs/main/linux-64::ca-certificates-2025.7.15-h06a4308_0 \n",
" cairo pkgs/main/linux-64::cairo-1.16.0-h44eff21_7 \n",
" certifi pkgs/main/linux-64::certifi-2025.8.3-py312h06a4308_0 \n",
" cffi pkgs/main/linux-64::cffi-1.17.1-py312h1fdaa30_1 \n",
" charset-normalizer pkgs/main/noarch::charset-normalizer-3.3.2-pyhd3eb1b0_0 \n",
" cuda-cudart nvidia/linux-64::cuda-cudart-12.4.127-0 \n",
" cuda-cupti nvidia/linux-64::cuda-cupti-12.4.127-0 \n",
" cuda-libraries nvidia/linux-64::cuda-libraries-12.4.1-0 \n",
" cuda-nvrtc nvidia/linux-64::cuda-nvrtc-12.4.127-0 \n",
" cuda-nvtx nvidia/linux-64::cuda-nvtx-12.4.127-0 \n",
" cuda-opencl nvidia/linux-64::cuda-opencl-12.9.19-0 \n",
" cuda-runtime nvidia/linux-64::cuda-runtime-12.4.1-0 \n",
" cuda-version nvidia/noarch::cuda-version-12.9-3 \n",
" dav1d pkgs/main/linux-64::dav1d-1.2.1-h5eee18b_0 \n",
" expat pkgs/main/linux-64::expat-2.7.1-h6a678d5_0 \n",
" ffmpeg pytorch/linux-64::ffmpeg-4.3-hf484d3e_0 \n",
" filelock pkgs/main/linux-64::filelock-3.17.0-py312h06a4308_0 \n",
" fontconfig pkgs/main/linux-64::fontconfig-2.14.1-h55d465d_3 \n",
" freetype pkgs/main/linux-64::freetype-2.13.3-h4a9f257_0 \n",
" fribidi pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0 \n",
" giflib pkgs/main/linux-64::giflib-5.2.2-h5eee18b_0 \n",
" gmp pkgs/main/linux-64::gmp-6.3.0-h6a678d5_0 \n",
" gmpy2 pkgs/main/linux-64::gmpy2-2.2.1-py312h5eee18b_0 \n",
" gnutls pkgs/main/linux-64::gnutls-3.6.15-he1e5248_0 \n",
" graphite2 pkgs/main/linux-64::graphite2-1.3.14-h295c915_1 \n",
" harfbuzz pkgs/main/linux-64::harfbuzz-10.2.0-hdfddeaa_1 \n",
" icu pkgs/main/linux-64::icu-73.1-h6a678d5_0 \n",
" idna pkgs/main/linux-64::idna-3.7-py312h06a4308_0 \n",
" intel-openmp pkgs/main/linux-64::intel-openmp-2023.1.0-hdb19cb5_46306 \n",
" jinja2 pkgs/main/linux-64::jinja2-3.1.6-py312h06a4308_0 \n",
" jpeg pkgs/main/linux-64::jpeg-9e-h5eee18b_3 \n",
" lame pkgs/main/linux-64::lame-3.100-h7b6447c_0 \n",
" lcms2 pkgs/main/linux-64::lcms2-2.16-h92b89f2_1 \n",
" ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.40-h12ee557_0 \n",
" lerc pkgs/main/linux-64::lerc-4.0.0-h6a678d5_0 \n",
" libavif pkgs/main/linux-64::libavif-1.1.1-h5eee18b_0 \n",
" libcublas nvidia/linux-64::libcublas-12.4.5.8-0 \n",
" libcufft nvidia/linux-64::libcufft-11.2.1.3-0 \n",
" libcufile nvidia/linux-64::libcufile-1.14.1.1-4 \n",
" libcurand nvidia/linux-64::libcurand-10.3.10.19-0 \n",
" libcusolver nvidia/linux-64::libcusolver-11.6.1.9-0 \n",
" libcusparse nvidia/linux-64::libcusparse-12.3.1.170-0 \n",
" libdeflate pkgs/main/linux-64::libdeflate-1.22-h5eee18b_0 \n",
" libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_1 \n",
" libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 \n",
" libglib pkgs/main/linux-64::libglib-2.84.2-h37c7471_0 \n",
" libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 \n",
" libiconv pkgs/main/linux-64::libiconv-1.16-h5eee18b_3 \n",
" libidn2 pkgs/main/linux-64::libidn2-2.3.4-h5eee18b_0 \n",
" libjpeg-turbo pytorch/linux-64::libjpeg-turbo-2.0.0-h9bf148f_0 \n",
" libnpp nvidia/linux-64::libnpp-12.2.5.30-0 \n",
" libnvfatbin nvidia/linux-64::libnvfatbin-12.9.82-0 \n",
" libnvjitlink nvidia/linux-64::libnvjitlink-12.4.127-0 \n",
" libnvjpeg nvidia/linux-64::libnvjpeg-12.3.1.117-0 \n",
" libpng pkgs/main/linux-64::libpng-1.6.39-h5eee18b_0 \n",
" libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 \n",
" libtasn1 pkgs/main/linux-64::libtasn1-4.19.0-h5eee18b_0 \n",
" libtiff pkgs/main/linux-64::libtiff-4.7.0-hde9077f_0 \n",
" libunistring pkgs/main/linux-64::libunistring-0.9.10-h27cfd23_0 \n",
" libuuid pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 \n",
" libwebp pkgs/main/linux-64::libwebp-1.3.2-h9f374a3_1 \n",
" libwebp-base pkgs/main/linux-64::libwebp-base-1.3.2-h5eee18b_1 \n",
" libxcb pkgs/main/linux-64::libxcb-1.17.0-h9b100fa_0 \n",
" libxml2 pkgs/main/linux-64::libxml2-2.13.8-hfdd30dd_0 \n",
" llvm-openmp pkgs/main/linux-64::llvm-openmp-14.0.6-h9e868ea_0 \n",
" lz4-c pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_1 \n",
" markupsafe pkgs/main/linux-64::markupsafe-3.0.2-py312h5eee18b_0 \n",
" mkl pkgs/main/linux-64::mkl-2023.1.0-h213fc3f_46344 \n",
" mkl-service pkgs/main/linux-64::mkl-service-2.4.0-py312h5eee18b_2 \n",
" mkl_fft pkgs/main/linux-64::mkl_fft-1.3.11-py312h5eee18b_0 \n",
" mkl_random pkgs/main/linux-64::mkl_random-1.2.8-py312h526ad5a_0 \n",
" mpc pkgs/main/linux-64::mpc-1.3.1-h5eee18b_0 \n",
" mpfr pkgs/main/linux-64::mpfr-4.2.1-h5eee18b_0 \n",
" mpmath pkgs/main/linux-64::mpmath-1.3.0-py312h06a4308_0 \n",
" ncurses pkgs/main/linux-64::ncurses-6.5-h7934f7d_0 \n",
" nettle pkgs/main/linux-64::nettle-3.7.3-hbbd107a_1 \n",
" networkx pkgs/main/linux-64::networkx-3.4.2-py312h06a4308_0 \n",
" numpy pkgs/main/linux-64::numpy-2.3.1-py312h2470af2_0 \n",
" numpy-base pkgs/main/linux-64::numpy-base-2.3.1-py312h06ae042_0 \n",
" ocl-icd pkgs/main/linux-64::ocl-icd-2.3.2-h5eee18b_1 \n",
" openh264 pkgs/main/linux-64::openh264-2.1.1-h4ff587b_0 \n",
" openjpeg pkgs/main/linux-64::openjpeg-2.5.2-h0d4d230_1 \n",
" openssl pkgs/main/linux-64::openssl-3.0.17-h5eee18b_0 \n",
" pcre2 pkgs/main/linux-64::pcre2-10.42-hebb0a14_1 \n",
" pillow pkgs/main/linux-64::pillow-11.3.0-py312hb1c3d2d_0 \n",
" pip pkgs/main/noarch::pip-25.1-pyhc872135_2 \n",
" pixman pkgs/main/linux-64::pixman-0.46.4-h7934f7d_0 \n",
" pthread-stubs pkgs/main/linux-64::pthread-stubs-0.3-h0ce48e5_1 \n",
" pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0 \n",
" pysocks pkgs/main/linux-64::pysocks-1.7.1-py312h06a4308_0 \n",
" python pkgs/main/linux-64::python-3.12.11-h22baa00_0 \n",
" pytorch pytorch/linux-64::pytorch-2.5.1-py3.12_cuda12.4_cudnn9.1.0_0 \n",
" pytorch-cuda pytorch/linux-64::pytorch-cuda-12.4-hc786d27_7 \n",
" pytorch-mutex pytorch/noarch::pytorch-mutex-1.0-cuda \n",
" pyyaml pkgs/main/linux-64::pyyaml-6.0.2-py312h5eee18b_0 \n",
" readline pkgs/main/linux-64::readline-8.3-hc2a1206_0 \n",
" requests pkgs/main/linux-64::requests-2.32.4-py312h06a4308_0 \n",
" setuptools pkgs/main/linux-64::setuptools-72.1.0-py312h06a4308_0 \n",
" sqlite pkgs/main/linux-64::sqlite-3.50.2-hb25bd0a_1 \n",
" sympy pkgs/main/linux-64::sympy-1.13.3-py312h06a4308_1 \n",
" tbb pkgs/main/linux-64::tbb-2021.8.0-hdb19cb5_0 \n",
" tk pkgs/main/linux-64::tk-8.6.15-h54e0aa7_0 \n",
" torchaudio pytorch/linux-64::torchaudio-2.5.1-py312_cu124 \n",
" torchtriton pytorch/linux-64::torchtriton-3.1.0-py312 \n",
" torchvision pytorch/linux-64::torchvision-0.20.1-py312_cu124 \n",
" typing_extensions pkgs/main/linux-64::typing_extensions-4.12.2-py312h06a4308_0 \n",
" tzdata pkgs/main/noarch::tzdata-2025b-h04d1e81_0 \n",
" urllib3 pkgs/main/linux-64::urllib3-2.5.0-py312h06a4308_0 \n",
" wheel pkgs/main/linux-64::wheel-0.45.1-py312h06a4308_0 \n",
" xorg-libx11 pkgs/main/linux-64::xorg-libx11-1.8.12-h9b100fa_1 \n",
" xorg-libxau pkgs/main/linux-64::xorg-libxau-1.0.12-h9b100fa_0 \n",
" xorg-libxdmcp pkgs/main/linux-64::xorg-libxdmcp-1.1.5-h9b100fa_0 \n",
" xorg-libxext pkgs/main/linux-64::xorg-libxext-1.3.6-h9b100fa_0 \n",
" xorg-libxrender pkgs/main/linux-64::xorg-libxrender-0.9.12-h9b100fa_0 \n",
" xorg-xorgproto pkgs/main/linux-64::xorg-xorgproto-2024.1-h5eee18b_1 \n",
" xz pkgs/main/linux-64::xz-5.6.4-h5eee18b_1 \n",
" yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 \n",
" zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_1 \n",
" zstd pkgs/main/linux-64::zstd-1.5.6-hc292b87_0 \n",
"\n",
"\n",
"Preparing transaction: ...working... done\n",
"Verifying transaction: ...working... done\n",
"Executing transaction: ...working... done\n"
]
}
],
"source": [
"!/opt/conda/condabin/conda create -n myenv -qy pytorch==2.5.1 torchvision==0.20.1 torchaudio==2.5.1 pytorch-cuda=12.4 -c pytorch -c nvidia"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "96f42d22-4108-4e99-9e25-ffe985204bea",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "b7be613d-18cd-46a2-859d-7f474012f28e",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "607cf1f1-aa0b-434b-a846-a20ae5326795",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "5039dfa0-c67b-4027-b6e1-741cc4b5aa35",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "ac3703f6-2b16-43ca-ba49-cbbfd498e7f0",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

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{
"cells": [
{
"cell_type": "markdown",
"id": "0f334e9f-b70a-44ff-9efd-d8638071d0c2",
"metadata": {},
"source": [
"Set env and make link for easier access"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "905f963a-d05a-49ea-a03a-05de2781f92d",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"env: PIP_CACHE_DIR=\"/home/pipcache\"\n",
"env: TOTALSEG_HOME_DIR=/home/pipcache/.totalsegmentator\n"
]
}
],
"source": [
"%env PIP_CACHE_DIR=\"/home/pipcache\"\n",
"%env TOTALSEG_HOME_DIR=/home/pipcache/.totalsegmentator\n",
"!ln -sf /Public ~"
]
},
{
"cell_type": "markdown",
"id": "200f91cb-71db-4600-872f-110ea269145c",
"metadata": {},
"source": [
"Check env"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "683c8515-79a5-4828-897e-9d635fc4136e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\"/home/pipcache\"\n",
"/home/pipcache/.totalsegmentator\n"
]
}
],
"source": [
"!echo $PIP_CACHE_DIR\n",
"!echo $TOTALSEG_HOME_DIR"
]
},
{
"cell_type": "markdown",
"id": "379d97dc-6fdf-4dd0-b250-23373e249d53",
"metadata": {},
"source": [
"Install PyTorch"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "e515f788-a539-43c9-b414-f4abd38e83c8",
"metadata": {},
"outputs": [],
"source": [
"!pip3 install -q \"torch<2.6.0\" torchvision"
]
},
{
"cell_type": "markdown",
"id": "3a5c47ba-56b3-4ed8-a897-c3ee980bcc94",
"metadata": {},
"source": [
"Install Totalsegmentator"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "1f4e0f6b-406b-4195-b110-fa398a68f54c",
"metadata": {},
"outputs": [],
"source": [
"!pip install -q TotalSegmentator"
]
},
{
"cell_type": "markdown",
"id": "053f9e40-1af5-4a0d-897a-69620d2410bf",
"metadata": {},
"source": [
"Segment body parts\n",
"set --device gpu: (0-7)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "ce1f9a94-dbd0-4820-bc52-7bb721923e0e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024\n",
"\n",
"Resampling...\n",
" Resampled in 14.70s\n",
"Predicting part 1 of 5 ...\n",
"100%|███████████████████████████████████████████| 27/27 [00:02<00:00, 11.13it/s]\n",
"Predicting part 2 of 5 ...\n",
"100%|███████████████████████████████████████████| 27/27 [00:01<00:00, 26.99it/s]\n",
"Predicting part 3 of 5 ...\n",
"100%|███████████████████████████████████████████| 27/27 [00:00<00:00, 27.85it/s]\n",
"Predicting part 4 of 5 ...\n",
"100%|███████████████████████████████████████████| 27/27 [00:00<00:00, 27.37it/s]\n",
"Predicting part 5 of 5 ...\n",
"100%|███████████████████████████████████████████| 27/27 [00:00<00:00, 27.90it/s]\n",
" Predicted in 98.29s\n",
"Resampling...\n",
"Saving segmentations...\n",
" Saved in 30.31s\n"
]
}
],
"source": [
"!~/.local/bin/TotalSegmentator --device gpu:1 -i /Public/inference/colon/1.3.6.1.4.1.9328.50.4.0001.nii.gz -o segmentations"
]
},
{
"cell_type": "markdown",
"id": "065e6132-e58f-4128-b452-44af56d5222e",
"metadata": {},
"source": [
"Segment teeth"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "f32e7987-1c0e-4fbe-b595-194cad661c58",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024\n",
"\n",
"Generating rough segmentation for cropping...\n",
"\n",
"If you use this tool please cite: https://pubs.rsna.org/doi/10.1148/ryai.230024\n",
"\n",
"Generating rough segmentation for cropping...\n",
"Resampling...\n",
" Resampled in 3.94s\n",
"Predicting...\n",
"100%|█████████████████████████████████████████████| 1/1 [00:00<00:00, 1.77it/s]\n",
" Predicted in 8.46s\n",
"Resampling...\n",
" cropping from (512, 512, 262) to (439, 486, 262)\n",
"Resampling...\n",
" Resampled in 6.55s\n",
"Predicting...\n",
"100%|███████████████████████████████████████████| 24/24 [00:02<00:00, 11.85it/s]\n",
" Predicted in 11.34s\n",
"Resampling...\n",
" cropping from (512, 512, 262) to (260, 244, 210)\n",
"Resampling...\n",
" Resampled in 1.45s\n",
"Predicting...\n",
"100%|█████████████████████████████████████████████| 3/3 [00:01<00:00, 2.85it/s]\n",
" Predicted in 12.05s\n",
"Resampling...\n",
"Saving segmentations...\n",
"Creating lower_jawbone.nii.gz\n",
"Creating upper_jawbone.nii.gz\n",
"Creating left_inferior_alveolar_canal.nii.gz\n",
"Creating right_inferior_alveolar_canal.nii.gz\n",
"Creating right_maxillary_sinus.nii.gz\n",
"Creating left_maxillary_sinus.nii.gz\n",
"Creating pharynx.nii.gz\n",
"Creating bridge.nii.gz\n",
"Creating crown.nii.gz\n",
"Creating implant.nii.gz\n",
"Creating upper_right_central_incisor_fdi11.nii.gz\n",
"Creating upper_right_lateral_incisor_fdi12.nii.gz\n",
"Creating upper_right_canine_fdi13.nii.gz\n",
"Creating upper_right_first_premolar_fdi14.nii.gz\n",
"Creating upper_right_second_premolar_fdi15.nii.gz\n",
"Creating upper_right_first_molar_fdi16.nii.gz\n",
"Creating upper_right_second_molar_fdi17.nii.gz\n",
"Creating upper_right_third_molar_fdi18.nii.gz\n",
"Creating upper_left_central_incisor_fdi21.nii.gz\n",
"Creating upper_left_lateral_incisor_fdi22.nii.gz\n",
"Creating upper_left_canine_fdi23.nii.gz\n",
"Creating upper_left_first_premolar_fdi24.nii.gz\n",
"Creating upper_left_second_premolar_fdi25.nii.gz\n",
"Creating upper_left_first_molar_fdi26.nii.gz\n",
"Creating upper_left_second_molar_fdi27.nii.gz\n",
"Creating upper_left_third_molar_fdi28.nii.gz\n",
"Creating lower_left_central_incisor_fdi31.nii.gz\n",
"Creating lower_left_lateral_incisor_fdi32.nii.gz\n",
"Creating lower_left_canine_fdi33.nii.gz\n",
"Creating lower_left_first_premolar_fdi34.nii.gz\n",
"Creating lower_left_second_premolar_fdi35.nii.gz\n",
"Creating lower_left_first_molar_fdi36.nii.gz\n",
"Creating lower_left_second_molar_fdi37.nii.gz\n",
"Creating lower_left_third_molar_fdi38.nii.gz\n",
"Creating lower_right_central_incisor_fdi41.nii.gz\n",
"Creating lower_right_lateral_incisor_fdi42.nii.gz\n",
"Creating lower_right_canine_fdi43.nii.gz\n",
"Creating lower_right_first_premolar_fdi44.nii.gz\n",
"Creating lower_right_second_premolar_fdi45.nii.gz\n",
"Creating lower_right_first_molar_fdi46.nii.gz\n",
"Creating lower_right_second_molar_fdi47.nii.gz\n",
"Creating lower_right_third_molar_fdi48.nii.gz\n",
"Creating left_mandibular_incisive_canal_fdi103.nii.gz\n",
"Creating right_mandibular_incisive_canal_fdi104.nii.gz\n",
"Creating lingual_canal.nii.gz\n",
"Creating upper_right_central_incisor_pulp_fdi111.nii.gz\n",
"Creating upper_right_lateral_incisor_pulp_fdi112.nii.gz\n",
"Creating upper_right_canine_pulp_fdi113.nii.gz\n",
"Creating upper_right_first_premolar_pulp_fdi114.nii.gz\n",
"Creating upper_right_second_premolar_pulp_fdi115.nii.gz\n",
"Creating upper_right_first_molar_pulp_fdi116.nii.gz\n",
"Creating upper_right_second_molar_pulp_fdi117.nii.gz\n",
"Creating upper_right_third_molar_pulp_fdi118.nii.gz\n",
"Creating upper_left_central_incisor_pulp_fdi121.nii.gz\n",
"Creating upper_left_lateral_incisor_pulp_fdi122.nii.gz\n",
"Creating upper_left_canine_pulp_fdi123.nii.gz\n",
"Creating upper_left_first_premolar_pulp_fdi124.nii.gz\n",
"Creating upper_left_second_premolar_pulp_fdi125.nii.gz\n",
"Creating upper_left_first_molar_pulp_fdi126.nii.gz\n",
"Creating upper_left_second_molar_pulp_fdi127.nii.gz\n",
"Creating upper_left_third_molar_pulp_fdi128.nii.gz\n",
"Creating lower_left_central_incisor_pulp_fdi131.nii.gz\n",
"Creating lower_left_lateral_incisor_pulp_fdi132.nii.gz\n",
"Creating lower_left_canine_pulp_fdi133.nii.gz\n",
"Creating lower_left_first_premolar_pulp_fdi134.nii.gz\n",
"Creating lower_left_second_premolar_pulp_fdi135.nii.gz\n",
"Creating lower_left_first_molar_pulp_fdi136.nii.gz\n",
"Creating lower_left_second_molar_pulp_fdi137.nii.gz\n",
"Creating lower_left_third_molar_pulp_fdi138.nii.gz\n",
"Creating lower_right_central_incisor_pulp_fdi141.nii.gz\n",
"Creating lower_right_lateral_incisor_pulp_fdi142.nii.gz\n",
"Creating lower_right_canine_pulp_fdi143.nii.gz\n",
"Creating lower_right_first_premolar_pulp_fdi144.nii.gz\n",
"Creating lower_right_second_premolar_pulp_fdi145.nii.gz\n",
"Creating lower_right_first_molar_pulp_fdi146.nii.gz\n",
"Creating lower_right_second_molar_pulp_fdi147.nii.gz\n",
"Creating lower_right_third_molar_pulp_fdi148.nii.gz\n",
" Saved in 27.18s\n"
]
}
],
"source": [
"!~/.local/bin/TotalSegmentator --device gpu:1 -i /Public/inference/ToothFairy3/ToothFairy3F_001_0000.nii.gz -o teeth --task teeth"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "650ea877-9f69-4ebd-82b1-a6e588957c29",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"id": "864afbe7-aee9-45ed-a96c-0a102899e1d7",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
}