diff --git a/task1-conda.ipynb b/task1-conda.ipynb new file mode 100644 index 0000000..31ff857 --- /dev/null +++ b/task1-conda.ipynb @@ -0,0 +1,262 @@ +{ + "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 +} diff --git a/task1-pip.ipynb b/task1-pip.ipynb new file mode 100644 index 0000000..efa6e0d --- /dev/null +++ b/task1-pip.ipynb @@ -0,0 +1,311 @@ +{ + "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 +}