NIH MEG Short Course 2018 - Revision history

Tomh: /* Support tools */

2023-09-20T17:35:04Z

Support tools

← Older revision		Revision as of 13:35, 20 September 2023
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	=====Support tools=====		=====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]		: [[CTF Tools \| Singularity container download]]

	* Text editors available within the container for editing shell scripts: vim, nano, gedit
	: {\| width=70% style="border: 1px solid black;"
	\|<u>Usage</u>: 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)
	\|}
	----		----

Amnamyst: Amnamyst moved page NIH MEG Course to NIH MEG Short Course 2018 without leaving a redirect: Archiving old page and moving to training section

2021-12-08T19:37:31Z

Amnamyst moved page NIH MEG Course to NIH MEG Short Course 2018 without leaving a redirect: Archiving old page and moving to training section

← Older revision	Revision as of 15:37, 8 December 2021
(No difference)

Amnamyst: Removed data directory directions (outdated)

2021-12-08T19:36:31Z

Removed data directory directions (outdated)

← Older revision		Revision as of 15:36, 8 December 2021
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	\|}		\|}

	=====Support tools ~~for the hands-on training sessions~~=====		=====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]
Line 36:		Line 36:
	\|-		\|-
	\| (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
	\|-
	\|}		\|}
	----		----

Amnamyst at 19:33, 8 December 2021

2021-12-08T19:33:42Z

← Older revision		Revision as of 15:33, 8 December 2021
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	\| 7. Tom Holroyd \|\|[[Media:Source_Localization.pdf\|Synthetic Aperture Magnetometry Workflow]]		\| 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~~		\| 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~~		\| 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~~		\| 10. Allison Nugent \|\| [[Media:Tutorial6_Connectivity.pdf\|Advanced (and potentially dangerous) topics]]
	\|-		\|-
	\|}		\|}

Amnamyst: Revising Page and Archiving Schedule

2021-12-08T19:31:18Z

Revising Page and Archiving Schedule

← Older revision		Revision as of 15:31, 8 December 2021
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	==MEG Short Course Agenda and Handouts:==		==MEG Short Course Agenda and Handouts:==

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

	Building 10 FAES Classroom 3: B1C207
	{\| class = "wikitable"		{\| class = "wikitable"
	\|~~12:30 –~~ 1~~:10~~ pm \|\|[[Media:MEG_Intro.pdf\|MEG: The Basics]] ~~<br/> Fred Carver~~		\| 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~~		\| 2. Tom Holroyd \|\|[[Media:Intro_to_SAM.pdf\|Introduction to Source Localization]]
	\|-		\|-
		⚫	\| 3. Stephen Robinson \|\|[[Media:InstrumentationLecture.pdf\|Instrumentation and Hardware]]
	\|1:50 – 2:00 pm \|\| Break
	\|-		\|-
		⚫	\| 4. Allison Nugent \|\|[[Media:MEG_Applications.pdf\|Applications: What can I do with MEG?]]
⚫	\|~~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
	\|}

	=====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~~
	\|-		\|-
		⚫	\| 5. Allison Nugent \|\|[[Media:Tutorial1_DataEditorPreprocessing.pdf\|Data Editor and command line Preprocessing]]
⚫	\|~~12:50~~ – ~~1:30~~ pm \|\|[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf\|Placing fiducials, headmodel creation]] ~~<br/> Allison Nugent~~
	\|-		\|-
		⚫	\| 6. Allison Nugent \|\|[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf\|Placing fiducials, headmodel creation]]
⚫	\|~~1:30~~ – ~~1:50~~ pm \|\|[[Media:Source_Localization.pdf\|Synthetic Aperture Magnetometry Workflow]]~~<br/> Tom Holroyd~~
	\|-		\|-
		⚫	\| 7. Tom Holroyd \|\|[[Media:Source_Localization.pdf\|Synthetic Aperture Magnetometry Workflow]]
	\|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		\|2:00 – 2:30 pm \|\| Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d <br/> Tom Holroyd

Amnamyst at 16:26, 8 October 2021

2021-10-08T16:26:10Z

← Older revision		Revision as of 12:26, 8 October 2021
Line 1:		Line 1:
	==MEG Short Course Agenda and Handouts:==		==MEG Short Course Agenda and Handouts:==

	=====Monday, August 6th=====		=====Monday, August 6th, 2018=====
	Building 10 FAES Classroom 3: B1C207		Building 10 FAES Classroom 3: B1C207
	{\| class = "wikitable"		{\| class = "wikitable"
Line 17:		Line 17:
	\|}		\|}

	=====Tuesday, August 7th=====		=====Tuesday, August 7th, 2018=====
	Building 10 FAES Classroom 3: B1C207		Building 10 FAES Classroom 3: B1C207
	{\| class = "wikitable"		{\| class = "wikitable"

Tomh: /* Tuesday, August 7th */

2018-08-09T17:53:08Z

Tuesday, August 7th

← Older revision		Revision as of 13:53, 9 August 2018
Line 24:		Line 24:
	\|12:50 – 1:30 pm \|\|[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf\|Placing fiducials, headmodel creation]] <br/> Allison Nugent		\|12:50 – 1:30 pm \|\|[[Media:Tutorial2_MRIHeadmodelPreprocessing.pdf\|Placing fiducials, headmodel creation]] <br/> Allison Nugent
	\|-		\|-
	\|1:30 – 1:50 pm \|\| Synthetic Aperture Magnetometry Workflow <br/> Tom Holroyd		\|1:30 – 1:50 pm \|\|[[Media:Source_Localization.pdf\|Synthetic Aperture Magnetometry Workflow]]<br/> Tom Holroyd
	\|-		\|-
	\|1:50 – 2:00 pm \|\| Break		\|1:50 – 2:00 pm \|\| Break

Tomh: /* Monday, August 6th */

2018-08-09T17:45:35Z

Monday, August 6th

← Older revision		Revision as of 13:45, 9 August 2018
Line 6:		Line 6:
	\|12:30 – 1:10 pm \|\|[[Media:MEG_Intro.pdf\|MEG: The Basics]] <br/> Fred Carver		\|12:30 – 1:10 pm \|\|[[Media:MEG_Intro.pdf\|MEG: The Basics]] <br/> Fred Carver
	\|-		\|-
	\|1:10 – 1:50 pm \|\| Introduction to Source Localization<br/>Tom Holroyd		\|1:10 – 1:50 pm \|\|[[Media:Intro_to_SAM.pdf\|Introduction to Source Localization]]<br/>Tom Holroyd
	\|-		\|-
	\|1:50 – 2:00 pm \|\| Break		\|1:50 – 2:00 pm \|\| Break
	\|-		\|-
	\|2:00 – 2:40 pm \|\|Instrumentation and Hardware<br/>Stephen Robinson		\|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		\|2:40 – 3:20 pm \|\|[[Media:MEG_Applications.pdf\|Applications: What can I do with MEG?]] <br/> Allison Nugent

Nugenta: /* MEG Short Course Agenda and Handouts: */

2018-08-08T15:14:08Z

MEG Short Course Agenda and Handouts:

← Older revision		Revision as of 11:14, 8 August 2018
Line 4:		Line 4:
	Building 10 FAES Classroom 3: B1C207		Building 10 FAES Classroom 3: B1C207
	{\| class = "wikitable"		{\| class = "wikitable"
	\|12:30 – 1:10 pm \|\|MEG: The Basics <br/> Fred Carver		\|12:30 – 1:10 pm \|\|[[Media:MEG_Intro.pdf\|MEG: The Basics]] <br/> Fred Carver
	\|-		\|-
	\|1:10 – 1:50 pm \|\| Introduction to Source Localization<br/>Tom Holroyd		\|1:10 – 1:50 pm \|\| Introduction to Source Localization<br/>Tom Holroyd
Line 30:		Line 30:
	\|2:00 – 2:30 pm \|\| Voxel-wise power estimates: sam_cov, sam_wts, sam_3d, and sam_4d <br/> Tom Holroyd		\|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 \|\| Induced power: sam_3dc <br/> Fred Carver		\|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		\|3:00 – 3:30 pm \|\| [[Media:Tutorial6_Connectivity.pdf\|Advanced (and potentially dangerous) topics]] <br/> Allison Nugent

Nugenta: /* Support tools for the hands-on training sessions */

2018-08-08T01:43:13Z

Support tools for the hands-on training sessions

← Older revision		Revision as of 21:43, 7 August 2018
Line 48:		Line 48:
	\|}		\|}
	* Working on the NIH HPC systems		* Working on the NIH HPC systems
	: Data ~~will~~ be available in /data/classes/meg, along with all necessary scripts		: Data are still available in /data/classes/meg, along with all necessary scripts
	: Modules are now available for SAM (samsrcv3) and CTF (ctf).		: Modules are now available for SAM (samsrcv3) and CTF (ctf).
	: To begin:		: To begin:
	: {\| width=70% style="border: 1px solid black;"		: {\| 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
	\|-		\|-
		⚫	\| $ . init_course.sh
	\| Once logged in, access the course materials with:
	\|-		\|-
⚫	\| $ ~~source~~ init_course.sh
	\|}		\|}
	----		----