EpilepsyAnalysis - Revision history

Jstout at 18:18, 26 November 2019

2019-11-26T18:18:02Z

← Older revision		Revision as of 14:18, 26 November 2019
Line 1:		Line 1:
	~~'''~~Introduction~~'''<br>~~		====Introduction====
	Epilepsy analysis at the NIH is comprised of several components<br>		Epilepsy analysis at the NIH is comprised of several components<br>
	# Copy data from MEG server and MRI folder		# Copy data from MEG server and MRI folder
Line 9:		Line 9:
	# Coregistration of MRI data to the orthohull data		# Coregistration of MRI data to the orthohull data

			====Analysis Code and Configuration====
⚫	~~'''~~Details~~'''~~
			The current analysis pipeline is performed through several Jupyter notebooks that are found on the internal repository
			#Configure the computer MEG code dependencies
			https://megcore.nih.gov/index.php/Configuring_analysis_machine
			#Configure the epilepsy code
			https://megcore.nih.gov/index.php/Configuring_Epilepsy_Analysis

		⚫	====Details====
	# Copy data from server (MEG_do_01.sh)		# Copy data from server (MEG_do_01.sh)
	## Enter information into the MEG file (####FIX NAME)		## Enter information into the MEG file (####FIX NAME)

Jstout at 18:22, 22 October 2019

2019-10-22T18:22:44Z

← Older revision		Revision as of 14:22, 22 October 2019
Line 28:		Line 28:
	## Determine if the regions with high kurtosis contain epileptiform activity		## Determine if the regions with high kurtosis contain epileptiform activity

			# SAMepi parameters
			## Covariance 10-70 (20-70 or 30-100Hz)

	'''Software Requirements'''		'''Software Requirements'''

Jstout at 17:28, 18 October 2019

2019-10-18T17:28:54Z

← Older revision		Revision as of 13:28, 18 October 2019
Line 10:		Line 10:

	'''Details'''		'''Details'''
			# Copy data from server (MEG_do_01.sh)
			## Enter information into the MEG file (####FIX NAME)
			## Run MEG_do_01.sh $DATE to pull the MEG data from the MEG repository and process the DICOM data
	# Coregistration		# Coregistration
	## Add LPA, RPA, Nasion fiducials to the dataset		## Add LPA, RPA, Nasion fiducials to the dataset

Jstout at 14:34, 18 October 2019

2019-10-18T14:34:49Z

← Older revision		Revision as of 10:34, 18 October 2019
Line 1:		Line 1:
	'''Introduction'''<br>		'''Introduction'''<br>
	Epilepsy analysis at the NIH is comprised of 3 components<br>		Epilepsy analysis at the NIH is comprised of several components<br>
			# Copy data from MEG server and MRI folder
			# Coregistration
			# Beamformer Analysis
			# Kurtosis Analysis of virtual sensors
			# Ranking of virtual sensors
			# Review of sensor data and virtual sensors
			# Coregistration of MRI data to the orthohull data

			'''Details'''
	# Coregistration		# Coregistration
	## Add LPA, RPA, Nasion fiducials to the dataset		## Add LPA, RPA, Nasion fiducials to the dataset

Jstout at 14:29, 18 October 2019

2019-10-18T14:29:40Z

← Older revision		Revision as of 10:29, 18 October 2019
Line 1:		Line 1:
	'''Introduction'''<br>		'''Introduction'''<br>
	Epilepsy analysis at the NIH is comprised of 3 components<br>		Epilepsy analysis at the NIH is comprised of 3 components<br>
	1) Coregistration~~<br>~~		# Coregistration
			## Add LPA, RPA, Nasion fiducials to the dataset
⚫	2) SAM analysis~~<br>~~
			## MEG_do_02.sh
⚫	## Constrain orientation (beta power analysis)
			### Opens Afni for the marking of the tags
			### Runs orthohull to realign the MRI to be aligned along the LPA/RPA/Nasion axis
		⚫	# SAM analysis
		⚫	## Constrain orientation (beta power analysis)
	## Search for excess kurtosis		## Search for excess kurtosis
	## Mapping voxels with highest excess kurtosis		## Mapping voxels with highest excess kurtosis
	## Creating 'virtual sensors' at the locations with excessive kurtosis		## Creating 'virtual sensors' at the locations with excessive kurtosis
	## Reviewing the SAM virtual sensors along with the		# Reviewing the SAM virtual sensors along with the sensor timeseries
			## Open the CTF dataset using the CTF DataEditor (may need to be run through the singularity container if dependencies have not been met on the os)
			## Add SAM output (this will apply the sensor weights to create a virtual sensor time series)
			## Determine if the regions with high kurtosis contain epileptiform activity


			'''Software Requirements'''
			SAMscrV*
			MEG_do_0*.sh - These commands must be launched from the scripts dir as the commands use the pwd command to structure the processing paths and determine the location of the patient data

	'''Issues with installation'''		'''Issues with installation'''
			At the top level of SAM software, the make command must be run.
			The links to the compiled SAM binaries must

			SAMsrcV3 - requires python 2.7
			SAMsrcV5 - compiled for python 3.7+

Jstout: Created page with "'''Introduction'''
Epilepsy analysis at the NIH is comprised of 3 components
1) Coregistration
2) SAM analysis
## Constrain orientation (beta power analysis)..."

2019-10-18T14:09:27Z

Created page with "'''Introduction''' Epilepsy analysis at the NIH is comprised of 3 components 1) Coregistration 2) SAM analysis ## Constrain orientation (beta power analysis)..."

New page

'''Introduction''' 
Epilepsy analysis at the NIH is comprised of 3 components 
1) Coregistration 
2) SAM analysis 
## Constrain orientation (beta power analysis)
## Search for excess kurtosis
## Mapping voxels with highest excess kurtosis
## Creating 'virtual sensors' at the locations with excessive kurtosis
## Reviewing the SAM virtual sensors along with the

'''Issues with installation'''