{ "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 }