Meg information based connectivity coding session - Revision history

Jstout at 17:58, 12 August 2022

2022-08-12T17:58:35Z

← Older revision		Revision as of 13:58, 12 August 2022
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	#In python, frites_output_root=$(pwd)/frites_dset		#In python, frites_output_root=$(pwd)/frites_dset
	ipython		ipython
	from frites_connectivity_tutorial.~~load_dataset~~ import load_dataset		from frites_connectivity_tutorial.load_data import load_dataset
	dt = load_dataset(<<FRITES_OUTPUT_ROOT>>)		dt = load_dataset(<<FRITES_OUTPUT_ROOT>>)

2022-08-12T17:43:30Z

Use on Biowulf

← Older revision		Revision as of 13:43, 12 August 2022
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	#Make sure modules are loadable -- this can also be added to ~/.bashrc file		#Make sure modules are loadable -- this can also be added to ~/.bashrc file
	module use --append /data/MEGmodules/modulefiles		module use --append /data/MEGmodules/modulefiles
	module load ~~SAMsrcDEV~~		module load SAMsrcDev

	#Make the SAM beamformers and apply the symbolic transfer entropy		#Make the SAM beamformers and apply the symbolic transfer entropy

2022-08-12T16:54:55Z

← Older revision		Revision as of 12:54, 12 August 2022
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	git clone https://github.com/brainets/CookingFrites.git		git clone https://github.com/brainets/CookingFrites.git
	pip install frites		pip install frites

			===Use on biowulf===
			sinteractive --mem=12G --cpus-per-task=8
			module use --append /data/MEGmodules/modulefiles
			module load mne_spyder #loads mne/mne-bids/frites/frites_tutorial

	==SAM Symoblic Transfer Entropy Connectivity ==		==SAM Symoblic Transfer Entropy Connectivity ==

2022-08-12T16:09:50Z

Install in new environment (RECOMMENDED!):

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   jupyter lab
   #Once jupyter is open, the notebooks are in the notebooks folder
 ===Install in current environment (Better to use New environment as listed above!)-===

2022-08-12T15:29:57Z

Use on Biowulf

← Older revision		Revision as of 11:29, 12 August 2022
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	===Use on Biowulf===		===Use on Biowulf===
	#Log into biowulf		#Log into biowulf
	sinteractive --mem=6G --cpus-per-task=4		sinteractive --mem=6G --cpus-per-task=4 #You may need more mem/cpus
	#Make sure modules are loadable -- this can also be added to ~/.bashrc file		#Make sure modules are loadable -- this can also be added to ~/.bashrc file
	module use --append /data/MEGmodules/modulefiles		module use --append /data/MEGmodules/modulefiles

2022-08-12T15:29:18Z

SAM Symoblic Transfer Entropy Connectivity - (tutorial will be formalized by Friday)

← Older revision		Revision as of 11:29, 12 August 2022
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	pip install frites		pip install frites

	==SAM Symoblic Transfer Entropy Connectivity ~~- (tutorial will be formalized by Friday)~~==		==SAM Symoblic Transfer Entropy Connectivity ==
	===Background===		===Background===
	[https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Club MEG SAM Connectivity Presentation Recording]		[https://megcore.nih.gov/MEG/Robinson_InformationTheoryMEG_ClubMEG_03102022.mp4 Club MEG SAM Connectivity Presentation Recording]

2022-08-12T15:08:50Z

← Older revision		Revision as of 11:08, 12 August 2022
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	!Under Construction - will be finalized by Friday!

	We will be meeting virtually over Zoom from 1pm-3pm with breakout rooms for questions and collaboration <br>		We will be meeting virtually over Zoom from 1pm-3pm with breakout rooms for questions and collaboration <br>
	There will be a quick discussion~~/demo (10-20mins)~~ and some example data on biowulf. <br>		There will be a quick discussion and some example data on biowulf. <br>

	==FRITES toolbox==		==FRITES toolbox==

2022-08-12T15:07:51Z

Use on Biowulf

← Older revision		Revision as of 11:07, 12 August 2022
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	module load SAMsrcDEV		module load SAMsrcDEV

			#Make the SAM beamformers and apply the symbolic transfer entropy
	#This part is already done
	sam_cov ...		sam_cov ...
	sam_wts ...		sam_wts ...
	STEdelay ....		STEdelay ....

	cp *TESTDATA* (fix this part) Local folder

	Usage: STEdelay [options] Version 5.0 (64-bit) rev-1, Aug 10 2022		Usage: STEdelay [options] Version 5.0 (64-bit) rev-1, Aug 10 2022

2022-08-11T14:22:14Z

Recommendations

← Older revision		Revision as of 10:22, 11 August 2022
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	Output is a text file		Output is a text file
	Must determine an embedding dimension (4 as default) - the higher the embedding the more data needed		Must determine an embedding dimension (4 as default) - the higher the embedding the more data needed
	Minimal requirements (1Khz sampling rate and 300s of data)		Minimal requirements (>=1Khz sampling rate and >=300s of data)
	The inputs do not need to be brain regions (for example can compare STE between audio track to brain region)		The inputs do not need to be brain regions (for example can compare STE between audio track to brain region)

2022-08-11T14:21:40Z

Recommendations

← Older revision		Revision as of 10:21, 11 August 2022
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	====Recommendations====		====Recommendations====
	This process is a trigger-free process that estimates the symbolic transfer entropy (connectivity assessed by delayed propagation of signals) between two ROIs		This process is a trigger-free process that estimates the symbolic transfer entropy (connectivity assessed by delayed propagation of signals) between two ROIs
	70-185Hz has been tested		70-185Hz has been tested and is recommended as a filter band
	Use an atlas based input for the bivariate connectivity assessment		Use an atlas based input for the bivariate connectivity assessment (AAL atlas, Desikan K., Destreux...)
	SAMwts or Patch_wts to create the beamformer		SAMwts or Patch_wts to create the beamformer
	Output is a text file		Output is a text file