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