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FIX: update validator install
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‎PETBIDS-Onboarding2025/BIDS_conversion_tutorial_Colab.ipynb‎

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"id": "XpjaKOjI3VsN",
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"outputId": "41cbac46-7d21-414c-88d2-887903af0610"
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},
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"outputs": [],
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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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"Repo already cloned.\n",
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"remote: Enumerating objects: 7, done.\u001b[K\n",
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"remote: Counting objects: 100% (7/7), done.\u001b[K\n",
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"remote: Compressing objects: 100% (1/1), done.\u001b[K\n",
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"remote: Total 4 (delta 3), reused 4 (delta 3), pack-reused 0 (from 0)\u001b[K\n",
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"Unpacking objects: 100% (4/4), 2.50 KiB | 427.00 KiB/s, done.\n",
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"From https://github.com/openneuropet/outreach\n",
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" a4017c4..39f64d6 main -> origin/main\n",
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"Updating a4017c4..39f64d6\n",
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"Fast-forward\n",
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" .../BIDS_conversion_tutorial_Colab.ipynb | 1690 \u001b[32m++++++++\u001b[m\u001b[31m------------\u001b[m\n",
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" 1 file changed, 693 insertions(+), 997 deletions(-)\n",
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"Requirement already satisfied: nipype in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (1.8.6)\n",
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"Requirement already satisfied: jedi in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (0.18.1)\n",
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"Requirement already satisfied: numpy>=1.17 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from nipype) (1.24.3)\n",
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"Requirement already satisfied: simplejson>=3.8.0 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from nipype) (3.19.2)\n",
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"Requirement already satisfied: traits!=5.0,<6.4,>=4.6 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from nipype) (6.3.2)\n",
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"Requirement already satisfied: looseversion in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from nipype) (1.3.0)\n",
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"Requirement already satisfied: joblib<2.0.0,>=1.2.0 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (1.2.0)\n",
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"Requirement already satisfied: json-maj<0.0.9,>=0.0.8 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (0.0.8)\n",
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"Requirement already satisfied: openpyxl<4.0.0,>=3.0.9 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (3.0.10)\n",
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"Requirement already satisfied: pandas<2.0.0,>=1.4.4 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (1.5.3)\n",
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"Requirement already satisfied: pydicom<3.0.0,>=2.2.2 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (2.4.4)\n",
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"Requirement already satisfied: pyparsing<4.0.0,>=3.0.4 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (3.0.9)\n",
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"Requirement already satisfied: python-dotenv<0.20.0,>=0.19.1 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (0.19.2)\n",
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"Requirement already satisfied: pyxlsb<2.0.0,>=1.0.9 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pypet2bids) (1.0.10)\n",
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"Requirement already satisfied: requests in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from etelemetry>=0.2.0->nipype) (2.31.0)\n",
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"Requirement already satisfied: ci-info>=0.2 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from etelemetry>=0.2.0->nipype) (0.3.0)\n",
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"Requirement already satisfied: et_xmlfile in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from openpyxl<4.0.0,>=3.0.9->pypet2bids) (1.1.0)\n",
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"Requirement already satisfied: pytz>=2020.1 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from pandas<2.0.0,>=1.4.4->pypet2bids) (2023.3.post1)\n",
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"Requirement already satisfied: isodate<0.7.0,>=0.6.0 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from rdflib>=5.0.0->nipype) (0.6.1)\n",
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"Requirement already satisfied: idna<4,>=2.5 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from requests->etelemetry>=0.2.0->nipype) (3.4)\n",
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"Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from requests->etelemetry>=0.2.0->nipype) (1.26.16)\n",
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"Requirement already satisfied: certifi>=2017.4.17 in /Users/martinnorgaard/anaconda3/lib/python3.11/site-packages (from requests->etelemetry>=0.2.0->nipype) (2023.7.22)\n",
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"/bin/bash: apt-get: command not found\n",
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"######################################################################## 100.0%##################################### 96.4%\n",
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"Archive: /Users/martinnorgaard/.deno/bin/deno.zip\n",
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" inflating: /Users/martinnorgaard/.deno/bin/deno \n",
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"Deno was installed successfully to /Users/martinnorgaard/.deno/bin/deno\n",
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"\u001b[0G\u001b[2K\u001b[J\u001b[0G\u001b[2K\u001b[J\u001b[0G\u001b[2K\u001b[J\u001b[0G\u001b[2K\u001b[J\u001b[0m\u001b[32mDownload\u001b[0m ▰▰▱▱▱▱ [00:00] 0/3\n",
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"\u001b[0m\u001b[38;5;245m jsr:@deno/installer-shell-setup/meta.json\n",
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"\u001b[0m\u001b[0G\u001b[0G\u001b[2A\u001b[2K\u001b[J\u001b[?25l\u001b[G\u001b[0K\u001b[G\u001b[1m\u001b[34mEdit shell configs to add deno to the PATH?\u001b[39m\u001b[22m (Y/n) █\u001b[G"
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]
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}
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],
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"source": [
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"!if [ -d \"outreach\" ]; then echo \"Repo already cloned.\" && cd outreach && git pull && cd ..; else echo \"Collecting Outreach Repository\" && git clone https://github.com/openneuropet/outreach.git; fi\n",
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"from os.path import basename\n",
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}
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],
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"source": [
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"!npm install -g bids-validatorimport subprocess"
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"!npm install -g bids-validator"
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]
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},
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{
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"provenance": []
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},
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"kernelspec": {
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"display_name": "nifreeze",
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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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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.17"
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"version": "3.11.5"
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}
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},
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"nbformat": 4,

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