Difference between revisions of "NIH MEG Short Course 2018"

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==MEG Short Course Agenda and Handouts:==
 
==MEG Short Course Agenda and Handouts:==
  
=====Monday, August 6th, 2018=====
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This course was held August 6 and 7, 2018 at NIH. The course files are archived below:
Building 10 FAES Classroom 3: B1C207
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{| class = "wikitable"
 
{| class = "wikitable"
|12:30 – 1:10 pm ||[[Media:MEG_Intro.pdf|MEG: The Basics]] <br/> Fred Carver
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| 1. Fred Carver ||[[Media:MEG_Intro.pdf|MEG: The Basics]]  
|-
 
|1:10 – 1:50 pm ||[[Media:Intro_to_SAM.pdf|Introduction to Source Localization]]<br/>Tom Holroyd
 
|-
 
|1:50 – 2:00 pm || Break
 
 
|-
 
|-
|2:00 – 2:40 pm ||[[Media:InstrumentationLecture.pdf|Instrumentation and Hardware]]<br/>Stephen Robinson
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| 2. Tom Holroyd ||[[Media:Intro_to_SAM.pdf|Introduction to Source Localization]]
 
|-
 
|-
|2:40 – 3:20 pm ||[[Media:MEG_Applications.pdf|Applications: What can I do with MEG?]] <br/> Allison Nugent
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| 3. Stephen Robinson ||[[Media:InstrumentationLecture.pdf|Instrumentation and Hardware]]
 
|-
 
|-
|3:20 – 3:30 pm ||Final Questions
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| 4. Allison Nugent ||[[Media:MEG_Applications.pdf|Applications: What can I do with MEG?]]
|}
 
 
 
=====Tuesday, August 7th, 2018=====
 
Building 10 FAES Classroom 3: B1C207
 
{| class = "wikitable"
 
|12:30 – 12:50 pm ||[[Media:Tutorial1_DataEditorPreprocessing.pdf|Data Editor and command line Preprocessing]] <br/> Allison Nugent
 
 
|-
 
|-
|12:50 – 1:30 pm ||[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf|Placing fiducials, headmodel creation]] <br/> Allison Nugent
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| 5. Allison Nugent ||[[Media:Tutorial1_DataEditorPreprocessing.pdf|Data Editor and command line Preprocessing]]
 
|-
 
|-
|1:30 – 1:50 pm ||[[Media:Source_Localization.pdf|Synthetic Aperture Magnetometry Workflow]]<br/> Tom Holroyd
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| 6. Allison Nugent ||[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf|Placing fiducials, headmodel creation]]
 
|-
 
|-
|1:50 – 2:00 pm || Break
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| 7. Tom Holroyd ||[[Media:Source_Localization.pdf|Synthetic Aperture Magnetometry Workflow]]
 
|-
 
|-
|2:00 – 2:30 pm || Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d <br/> Tom Holroyd
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| 8. Tom Holroyd || Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d <br>(''Slides unavailable, but reach out to Tom for more information on this topic'')
 
|-
 
|-
|2:30 – 3:00 pm || [[Media:Tutorial5_SAMinducedpower.pdf|Induced power: sam_3dc]] <br/> Fred Carver
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| 9. Fred Carver || [[Media:Tutorial5_SAMinducedpower.pdf|Induced power: sam_3dc]]
 
|-
 
|-
|3:00 – 3:30 pm || [[Media:Tutorial6_Connectivity.pdf|Advanced (and potentially dangerous) topics]] <br/> Allison Nugent
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| 10. Allison Nugent || [[Media:Tutorial6_Connectivity.pdf|Advanced (and potentially dangerous) topics]]
 
|-
 
|-
 
|}
 
|}
  
=====Support tools for the hands-on training sessions=====
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=====Support tools=====
 
* Singularity container with the CTF DataEditor tool and the SAMsrc MEG tools running under CentOS 6.9
 
* Singularity container with the CTF DataEditor tool and the SAMsrc MEG tools running under CentOS 6.9
 
: [https://megcore.nih.gov/MEG/megcore.img Singularity container megcore.img download]
 
: [https://megcore.nih.gov/MEG/megcore.img Singularity container megcore.img download]
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|-
 
|-
 
| (your /home directory and the /tmp file systems are automatically visible inside the container)
 
| (your /home directory and the /tmp file systems are automatically visible inside the container)
|}
 
* Working on the NIH HPC systems
 
: Data are still available in /data/classes/meg, along with all necessary scripts
 
: Modules are now available for SAM (samsrcv3) and CTF (ctf).
 
: To begin:
 
: {| width=70% style="border: 1px solid black;"
 
| Copy the data from /data/classes/meg
 
|-
 
| Use the initialization script to configure your environment:
 
|-
 
| $ . init_course.sh
 
|-
 
 
|}
 
|}
 
----
 
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Latest revision as of 15:37, 8 December 2021

MEG Short Course Agenda and Handouts:

This course was held August 6 and 7, 2018 at NIH. The course files are archived below:

1. Fred Carver MEG: The Basics
2. Tom Holroyd Introduction to Source Localization
3. Stephen Robinson Instrumentation and Hardware
4. Allison Nugent Applications: What can I do with MEG?
5. Allison Nugent Data Editor and command line Preprocessing
6. Allison Nugent Placing fiducials, headmodel creation
7. Tom Holroyd Synthetic Aperture Magnetometry Workflow
8. Tom Holroyd Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d
(Slides unavailable, but reach out to Tom for more information on this topic)
9. Fred Carver Induced power: sam_3dc
10. Allison Nugent Advanced (and potentially dangerous) topics
Support tools
  • Singularity container with the CTF DataEditor tool and the SAMsrc MEG tools running under CentOS 6.9
Singularity container megcore.img download
  • Text editors available within the container for editing shell scripts: vim, nano, gedit
Usage: singularity shell --bind /data:/mnt/data megcore.img
where the /data file system holds your CTF data set and mounts under /mnt/data inside the container
(your /home directory and the /tmp file systems are automatically visible inside the container)