NIH MEG Short Course 2018: Difference between revisions

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==MEG Short Course Agenda and Handouts:==
 
=====Monday, August 6th=====
Building 10 FAES Classroom 3: B1C207
{| class = "wikitable"
|12:30 – 1:10 pm ||[[Media:MEG_Intro.pdf|MEG: The Basics]] <br/> Fred Carver
|-
|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
|-
|2:40 – 3:20 pm ||[[Media:MEG_Applications.pdf|Applications: What can I do with MEG?]] <br/> Allison Nugent
|-
|3:20 – 3:30 pm ||Final Questions
Line 20:
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
|-
|1:30 – 1:50 pm || [[Media:Source_Localization.pdf|Synthetic Aperture Magnetometry Workflow ]]<br/> Tom Holroyd
|-
|1:50 – 2:00 pm || Break
|-
|2:00 – 2:30 pm || Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d <br/> Tom Holroyd
|-
|2:30 – 3:00 pm || [[Media:Tutorial5_SAMinducedpower.pdf|Induced power: sam_3dc]] <br/> Fred Carver
|-
|3:00 – 3:30 pm || [[Media:Tutorial6_Connectivity.pdf|Advanced (and potentially dangerous) topics]] <br/> Allison Nugent
|-
|}
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|}
* Working on the NIH HPC systems
: Data willare bestill 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
| Log in to the student account (NN is 1--30):
|-
| Use the initialization script to configure your environment:
| $ ssh -Y studentNN@felix.nimh.nih.gov
|-
| $ source. init_course.sh▼
| Once logged in, access the course materials with:
|-
▲| $ source init_course.sh
|}
----

Revision as of 13:53, 9 August 2018

MEG Short Course Agenda and Handouts:

Monday, August 6th

Building 10 FAES Classroom 3: B1C207

12:30 – 1:10 pm MEG: The Basics
Fred Carver
1:10 – 1:50 pm Introduction to Source Localization
Tom Holroyd
1:50 – 2:00 pm Break
2:00 – 2:40 pm Instrumentation and Hardware
Stephen Robinson
2:40 – 3:20 pm Applications: What can I do with MEG?
Allison Nugent
3:20 – 3:30 pm Final Questions
Tuesday, August 7th

Building 10 FAES Classroom 3: B1C207

12:30 – 12:50 pm Data Editor and command line Preprocessing
Allison Nugent
12:50 – 1:30 pm Placing fiducials, headmodel creation
Allison Nugent
1:30 – 1:50 pm Synthetic Aperture Magnetometry Workflow
Tom Holroyd
1:50 – 2:00 pm Break
2:00 – 2:30 pm Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d
Tom Holroyd
2:30 – 3:00 pm Induced power: sam_3dc
Fred Carver
3:00 – 3:30 pm Advanced (and potentially dangerous) topics
Allison Nugent
Support tools for the hands-on training sessions
  • 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)
  • 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:
Copy the data from /data/classes/meg
Use the initialization script to configure your environment:
$ . init_course.sh
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