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permanent spacetop documentation
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‎docs/m05_documentation/documentation.md

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---
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layout: default
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title: Running experiments
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permalink: /runningexp
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nav_order: 4
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has_children: true
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---
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# Running experiments
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{: .no_toc }
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{: .fs-9 }
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Running experiments involves 3 components: 1) sticking to the protocols, 2) knowing how to set up equipment (fMRI PC, fMRI scan room, TSA-II, Biopac), and 3) running the spacetop task scripts (7 individual tasks)
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{: .fs-6 .fw-300 }
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{: toc }
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Fast links
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{: .fs-6 .fw-300 }
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links required per session
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{: .text-delta}
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[ST participants](https://docs.google.com/spreadsheets/d/18zKGZAWgs56yYbpeZ4GRV_EnNmQElBvT8M3sfeNBUmI/edit?usp=sharing){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
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[Daily setup checklist](https://docs.google.com/document/d/1Xj3KeMtZRq-R_-78stY_sAlMGLKBEqkvL2FKDcMgtzc/edit?usp=sharing){: .btn .fs-5 .mb-4 .mb-md-0 }
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links dependent on session
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{: .text-delta}
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[scan 1 protocol](https://docs.google.com/document/d/1cwrJDC7tmMO6fwplcRVyyn8tpM04JTQAVwdiWWCiHy4/edit?usp=sharing){: .btn .btn-blue .fs-3 .mb-4 .mb-md-0 .mr-2 }
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[scan 2 protocol](https://docs.google.com/document/d/1UUFopzMc_TJ1ou1UpR2AEMAMvkMaTE9fvH5HAcNx2Yw/edit?usp=sharing){: .btn .fs-3 .mb-4 .mb-md-0 .text-blue-000}
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[scan 3 protocol](https://docs.google.com/document/d/1Uq9PeuWD-UYfOlbo8buPV0LIJ9oI_Z7SVBPRbZjEobs/edit?usp=sharing){: .btn .btn-blue .fs-3 .mb-4 .mb-md-0 .mr-2 }
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[scan 4 protocol](https://docs.google.com/document/d/17upqAFQgOwlCh2EOxgbhVJjdnb6hi01mG9UOgyeIRHU/edit?usp=sharing){: .btn .fs-3 .mb-4 .mb-md-0 .text-blue-000}
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<!-- <span class="fs-3">
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[Tiny button](http://example.com/){: .btn }
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</span> -->

‎docs/m05_documentation/g01_stimuli.md

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---
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layout: default
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title: Protocols (DBIC + Testing 453)
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parent: Documentation
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permalink: /doc/stimuli
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nav_order: 1
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---
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# Protocols: fMRI + behavioral
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{: .no_toc }
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{: .fs-11 }
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<details open markdown="block">
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<summary>
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Table of contents
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</summary>
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{: .text-delta }
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1. TOC
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{:toc}
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</details>
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# fMRI protocols
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{: .d-inline-block}
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maintained by Luke
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{: .label .label-green }
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* [scan 1 master protocol](https://docs.google.com/document/d/1cwrJDC7tmMO6fwplcRVyyn8tpM04JTQAVwdiWWCiHy4/edit?usp=sharing){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
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* [scan 2 master protocol](https://docs.google.com/document/d/1UUFopzMc_TJ1ou1UpR2AEMAMvkMaTE9fvH5HAcNx2Yw/edit?usp=sharing){: .btn .fs-5 .mb-4 .mb-md-0 }
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* [scan 3 master protocol](https://docs.google.com/document/d/1Uq9PeuWD-UYfOlbo8buPV0LIJ9oI_Z7SVBPRbZjEobs/edit?usp=sharing){: .btn .btn-primary .fs-5 .mb-4 .mb-md-0 .mr-2 }
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* [scan 4 master protocol](https://docs.google.com/document/d/17upqAFQgOwlCh2EOxgbhVJjdnb6hi01mG9UOgyeIRHU/edit?usp=sharing){: .btn .fs-5 .mb-4 .mb-md-0 }
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---
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links dependent on session
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{: .text-delta}
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## session 1
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[scan 1 protocol](https://docs.google.com/document/d/1cwrJDC7tmMO6fwplcRVyyn8tpM04JTQAVwdiWWCiHy4/edit?usp=sharing)
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### behavioral
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* [spacetop overview (PPT)](https://drive.google.com/file/d/1Gqtk3tscjNDzrcNw-tYlWnoVyS6OGuBC/view?usp=sharing)
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* [social influence instructions (PPT)](https://drive.google.com/file/d/1NjwO1qHNQAufzUjs6xjFf_gb4p8qFHFt/view?usp=sharing)
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* bartoshuck scale practice (MATLAB): `C:\Users\Dartmouth College\Desktop\Spacetop\SpaceTop_Attribution_Learning-master`
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* Practice Align-Videos Task (MATLAB) https://github.com/spatialtopology/func_align_video_task/blob/master/code/practice_func_align_video_task.m
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### scanner
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* `Linux PC > repos > social_influence > scripts > `
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* `Linux PC > repos > video task`
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---
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## session 2
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[scan 2 protocol](https://docs.google.com/document/d/1UUFopzMc_TJ1ou1UpR2AEMAMvkMaTE9fvH5HAcNx2Yw/edit?usp=sharing){: .btn .fs-5 .mb-4 .mb-md-0 .text-blue-000}
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### prescan
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* [spacetop overview ppt](https://drive.google.com/file/d/1Gqtk3tscjNDzrcNw-tYlWnoVyS6OGuBC/view)
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* [narratives powerpoint]()
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* [face powerpoint]()
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### scanner
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* Linux PC > repos > faces
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* Linux PC > repos > narratives
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---
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## session 3
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[scan 3 protocol](https://docs.google.com/document/d/1Uq9PeuWD-UYfOlbo8buPV0LIJ9oI_Z7SVBPRbZjEobs/edit?usp=sharing){: .btn .btn-blue .fs-5 .mb-4 .mb-md-0 .mr-2 }
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### prescan
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* [spacetop overview ppt](https://drive.google.com/file/d/1Gqtk3tscjNDzrcNw-tYlWnoVyS6OGuBC/view)
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* [self-ref ppt](https://docs.google.com/presentation/d/1LaVPOmwckZEx68DAeqrkSNhKCkAQsJ0BL5puQePh5FI/edit)
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* Linux PC > repos > practice self-ref/self-other mat file
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* Linux PC > repos > video_viewing_only script
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* [learning instruction ppt](https://drive.google.com/file/d/1f_MwibCkFJ0U9OrQhAaGQsD5kBPN5f6z/view)
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* Linux PC > repos > learning > A01_learning_phase
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* ST participants for leg sites in learning task
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### scanner
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* Linux PC > repos > self other task
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* Linux PC > repos > learning A02
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### postscan
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* Linux PC > repos > learning A03
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---
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## session 4
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[scan 4 protocol](https://docs.google.com/document/d/17upqAFQgOwlCh2EOxgbhVJjdnb6hi01mG9UOgyeIRHU/edit?usp=sharing){: .btn .fs-5 .mb-4 .mb-md-0 .text-blue-000}
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### prescan
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* social influence reminder
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* Linux PC > repos > fractionals practice
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### scanner
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* Linux PC > repos > fractional
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* Linux PC > repos > social influence
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---
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# Task info + session checklists
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{: .d-inline-block }
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Coming soon
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{: .label .label-yellow }
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| | face | fractional| learning |narratives|self-other|social-influence| videos|
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|:-------|:------|:----------|:---------|:---------|:---------|:---------------|:---------|
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|device | button| button | trackball|button |trackball |trackball | trackball|
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|thermode| X | X | O | X | X | O | X |

‎docs/m05_documentation/g02_thermodes.md

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---
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layout: default
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title: Protocols
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parent: Documentation
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permalink: /doc/stimuli
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nav_order: 1
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---
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# Protocols
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{: .no_toc }
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{: .fs-11 }
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## Table of contents
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{: .no_toc .text-delta }
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1. TOC
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{: .no_toc}
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# Thermode rules
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# Plugging in programs
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# naming convention
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for standardization
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let's stick with
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`PROJECT_temp-XX_dur-XX_8bit-XX`
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* the 8 bit code is necessary - mind you, 8 bit codes cannot overlap.
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If you've plugged in numbers from 45-50, the next experimenter cannot use those numbers.
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In order to help the next experimenter, please indicate which 8bit codes you've used.
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We're not good with reading binary numbers - please indicate the decimal version
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# Manual trigger
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# participant login
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# checking thermode OUTPUT
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---
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# Social Influence parameters
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* ![social_47]({{ site.url }}/images/spacetop_social_47.png)
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* ![social_48]({{ site.url }}/images/spacetop_social_48.png)
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* ![social_49]({{ site.url }}/images/spacetop_social_49.png)
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---
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# Learning task parameters
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* ![learning_45]({{ site.url }}/images/spacetop_learning_45.png)
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* ![learning_46]({{ site.url }}/images/spacetop_learning_46.png)
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* ![learning_47]({{ site.url }}/images/spacetop_learning_47.png)
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* ![learning_48]({{ site.url }}/images/spacetop_learning_48.png)
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* ![learning_49]({{ site.url }}/images/spacetop_learning_49.png)
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* ![learning_50]({{ site.url }}/images/spacetop_learning_50.png)

‎docs/m05_documentation/g03_linuxsetup.md

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---
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layout: default
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title: Linux Laptop setup
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parent: Documentation
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permalink: /doc/lsetup
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nav_order: 5
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---
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# Linux Laptop Setup
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{: .no_toc }
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{: .fs-11 }
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<!-- ## Table of contents
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{: .no_toc .text-delta } -->
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<details open markdown="block">
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<summary>
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Table of contents
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</summary>
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{: .text-delta }
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1. TOC
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{:toc}
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</details>
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# Linux laptop setup
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step 1
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{: .label .label-blue}
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## Reason why we had to go with Linux
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{: .d-inline-block .fs-6}
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* developers of psychtoolbox recommend linux
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* timing issue with windows (lag icon)
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* added more than two minutes of a lag for a task
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* ease of containerization
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step 2
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{: .label .label-blue}
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# Installing PTB on linux
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{: .d-inline-block }
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move elsewhere
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{: .label .label-green}
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check installation
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* neurodebian
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* neurodocker
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* anaconda
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* singularity
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worked for Luke
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http://neuro.debian.net/install_pkg.html?p=psychtoolbox-3-common
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Yarik suggestion
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You need to add contrib (probably no need for non-free) portion in addition to main in your NeuroDebian apt file.
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* https://wiki.debian.org/SourcesList
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* `cat /etc/apt/sources.list.d/neurodebian.sources.list`
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Getting error message:
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> libGL error: MESA_LOADER: failed to open readeonsi (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri)
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libGL error: failed to load driver: readeonsi
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failed to create dri screen
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-> https://psychtoolbox.discourse.group/t/matlab-crashes-after-insatlling-ptb-com-jogamp-opengl-glexception/74
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# adding EOL to matlab path without having to add it everytime
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* check `sudo vim /etc/ptb3/matlab.sh`
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* added a matlab path:
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EOL MASTER = /home/spacetop/repos/EOL-master
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in the shell script
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add the line ```export MATLABPATH=$(find "$EOL_MASTER" -type d | grep -v private | tr '\n' ':')$MATLABPATH```
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## firewall
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* allow incoming input from medoc PC
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* use iptable
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* ```iptables -A OUTPUT -p tcp -d 192.168.0.114 --dport 20121 -j ACCEPT```
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* https://serverfault.com/questions/183461/how-do-i-allow-outgoing-connections-via-iptables
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## manually changing IP on linux
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* follow this page to change the ip. [link](https://www.linuxtechi.com/assign-static-ip-address-ubuntu-20-04-lts/#:~:text=Configuring%20a%20static%20ip%20address,and%20then%20choose%20wired%20settings.&text=In%20the%20next%20window%2C%20Choose,gateway%20and%20DNS%20Server%20IP.)
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* make sure to change the name of this ethernet setting:
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Wired > identity > name : spacetop.dartmouth.edu
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## Setting firewalls and allowing private network
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* ping the medoc PC from the spacetop stim PC
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* if it doesn't work, there are two things that need to happen
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>> Create a new rule:
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[creating rules](https://www.howtogeek.com/112564/how-to-create-advanced-firewall-rules-in-the-windows-firewall/)
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>> Frewall > Inbound rules > look for "file and printer sharing (echo Request - ICMPv4-In) Private" > Enable rule

‎docs/m05_documentation/g04_containers.md

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---
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layout: default
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title: Building Containers
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parent: Documentation
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permalink: /doc/containers
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nav_order: 4
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---
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# Building Containers
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{: .no_toc }
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{: .fs-11 }
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## Table of contents
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{: .no_toc .text-delta }
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1. TOC
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{:toc}
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---
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Containers aid reproducible research, while alleviating the pain of installing programs/packages every time you're working in a new environment.
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Docker and Singularity are platforms that allow you to build and execute containers.
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Reasons I had to build a container:
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I needed pymvpa and nilearn, which had to run on CU's cluster. This was around 2018, prior to the conda environment feature that is now enabled on Summit and Blanca. Hence, I needed a singularity container, instead of a docker container. However, converting a docker container to singularity is easy, once you have singularity on your local machine.
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---
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# 0. install singularity on your local machine
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Please check here.
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* https://singularity.lbl.gov/install-mac
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* https://singularity.lbl.gov/install-linux
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* https://singularity.lbl.gov/install-windows
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# 1. First start off with installing vagrant
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* where I've installed it: Documents/singularity-vm
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* change directory into it and run the following lines
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```
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cd ~/Documents/singularity-vm
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vagrant init singularityware/singularity-2.4
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vagrant up
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vagrant ssh
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```
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# 2. once you've logged into vagrant, we're going to build the container
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using singularity...
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`IMG` : name of the container
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You need to set the initial size of the image (container) 8000, i.e., 8 GB
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`DEF` : has the code that builds the containers
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```
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IMG="snaglab_pymvpa2_nilearn.img"
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DEF="debian.def"
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sudo rm -f $IMG
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sudo singularity create -s 8000 $IMG
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sudo singularity image.create -s 8000 $IMG
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sudo singularity bootstrap $IMG $DEF
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```
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# 3. create the singularity container
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copyout the container ( in local directory not virtual machine)
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```
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vagrant port `( in the folder where you've installed vagrant)`
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```
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from local dir
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```
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scp -P 2222 vagrant@127.0.0.1:/home/vagrant/snaglab_pymvpa2.img .
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scp -P 2222 vagrant@127.0.0.1:/home/vagrant/debian.def .
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scp -P 2222 vagrant@127.0.0.1:/home/vagrant/definition.def .
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```
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# 4. Build a docker container and convert it to singularity
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Example: I built FSL based on https://github.com/BIDS-Apps/dockerfile-templates/blob/master/FSL/Dockerfile
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go to the local directory where dockerfile exists
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```
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docker build -t fslnine .
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docker tag f6b20d2fbb99 jungheejung/fslnine:latest
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docker push jungheejung/fslnine:latest
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```
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If your HPC doesn't allow for docker, but has singularity,
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here's how to convert dockers into singularity containers.
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```
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docker run --privileged -t --rm \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v /Users/h/Documents/singularity-vm:/output \
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singularityware/docker2singularity \
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jungheejung/fslnine:latest
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```

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