Meg information based connectivity coding session: Difference between revisions
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cp ***TESTDATA*** (fix this part) Local folder |
cp ***TESTDATA*** (fix this part) Local folder |
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Usage: STEdelay [options] Version 5.0 (64-bit) rev-1, Aug 10 2022 |
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Options: |
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If a parameter begins with '--', it is allowed on the command line, |
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otherwise it is only allowed in a parameter file (see -m). |
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All times are in seconds. |
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-h, --help show this help |
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-r DSNAME, --DataSet DSNAME |
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MEG dataset name [env_var = ds] |
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-m PFILE, --param PFILE parameter file name (optionally ending |
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in ".param") [env_var = param] |
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-v, --verbose verbose output |
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--CovType GLOBAL|SUM|ALL which covariance matrix to use for the analysis |
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--CovBand LO HI covariance bandwidth limits in Hz |
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--ImageBand LO HI imaging covariance bandwidth limits in Hz |
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--OrientBand LO HI band to use for orientation instead of Global (Hz) |
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--SmoothBand LO HI used to smooth Hilbert envelope, kurtosis, or RVE (Hz) |
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--Notch apply a powerline notch |
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(including harmonics) |
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--Hz HZ frequency for powerline (Hz, default 60) |
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ImageMetric METRICSPEC imaging metric |
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--Extent DIST radial extent from ROI voxels or centroid (mm) |
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-t TARGETFILE, --TargetName TARGETFILE |
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file containing target coordinates |
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-i MRIDIR, --MRIDirectory MRIDIR |
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MRI directory root [env_var = mridir] |
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-o IMAGEDIR, --ImageDirectory IMAGEDIR |
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image output directory [env_var = imagedir] |
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--PrefixLength N DataSet prefix may be specified as a number |
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or as a prefix delimiter (default "_") |
Revision as of 10:20, 11 August 2022
!Under Construction - will be finalized by Friday!
We will be meeting virtually over Zoom from 1pm-3pm with breakout rooms for questions and collaboration
There will be a quick discussion/demo (10-20mins) and some example data on biowulf.
FRITES toolbox
Club MEG Presentation Recording
Background Getting Started Scripts Example Scripts
Install in new environment (RECOMMENDED!):
conda create -n frites conda-forge::mne conda-forge::jupyterlab pip -y conda activate frites pip install frites
git clone https://github.com/brainets/CookingFrites.git cd CookingFrites 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!)-
#Download getting started tutorials git clone https://github.com/brainets/CookingFrites.git pip install frites
SAM Symoblic Transfer Entropy Connectivity - (tutorial will be formalized by Friday)
Background
Club MEG SAM Connectivity Presentation Recording
Recommendations
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 Use an atlas based input for the bivariate connectivity assessment SAMwts or Patch_wts to create the beamformer Output is a text file 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) The inputs do not need to be brain regions (for example can compare STE between audio track to brain region)
Use on Biowulf
#Log into biowulf sinteractive --mem=6G --cpus-per-task=4 #Make sure modules are loadable -- this can also be added to ~/.bashrc file module use --append /data/MEGmodules/modulefiles module load SAMsrcDEV
#This part is already done sam_cov ... sam_wts ... STEdelay ....
cp ***TESTDATA*** (fix this part) Local folder
Usage: STEdelay [options] Version 5.0 (64-bit) rev-1, Aug 10 2022 Options: If a parameter begins with '--', it is allowed on the command line, otherwise it is only allowed in a parameter file (see -m). All times are in seconds. -h, --help show this help -r DSNAME, --DataSet DSNAME MEG dataset name [env_var = ds] -m PFILE, --param PFILE parameter file name (optionally ending in ".param") [env_var = param] -v, --verbose verbose output --CovType GLOBAL|SUM|ALL which covariance matrix to use for the analysis --CovBand LO HI covariance bandwidth limits in Hz --ImageBand LO HI imaging covariance bandwidth limits in Hz --OrientBand LO HI band to use for orientation instead of Global (Hz) --SmoothBand LO HI used to smooth Hilbert envelope, kurtosis, or RVE (Hz) --Notch apply a powerline notch (including harmonics) --Hz HZ frequency for powerline (Hz, default 60) ImageMetric METRICSPEC imaging metric --Extent DIST radial extent from ROI voxels or centroid (mm) -t TARGETFILE, --TargetName TARGETFILE file containing target coordinates -i MRIDIR, --MRIDirectory MRIDIR MRI directory root [env_var = mridir] -o IMAGEDIR, --ImageDirectory IMAGEDIR image output directory [env_var = imagedir] --PrefixLength N DataSet prefix may be specified as a number or as a prefix delimiter (default "_")