Configuring Epilepsy Analysis - Revision history

Jstout: /* Launching Review Software */

2019-11-27T00:20:26Z

Launching Review Software

← Older revision		Revision as of 20:20, 26 November 2019
Line 17:		Line 17:
	startup_epilepsy_review.sh		startup_epilepsy_review.sh
	Initializes BASH shell >> activates conda environment >> cd to Notebook Dir >> launches Jupyter Lab		Initializes BASH shell >> activates conda environment >> cd to Notebook Dir >> launches Jupyter Lab
			#Bash is not default on the review computer
			#Conda maintains non-conflicting python environments (can be reinitialized using environment.yml file in code folder)

	====Configuration Files====		====Configuration Files====

Jstout at 00:19, 27 November 2019

2019-11-27T00:19:06Z

← Older revision		Revision as of 20:19, 26 November 2019
Line 13:		Line 13:
	#/etc/profile.d/meg.sh (System Folder - requires sudo - may need to create file meg.sh)		#/etc/profile.d/meg.sh (System Folder - requires sudo - may need to create file meg.sh)
	export epil_code_path=$path_to_code #This is used in the python code to determine the location of config files in the data		export epil_code_path=$path_to_code #This is used in the python code to determine the location of config files in the data

			====Launching Review Software====
			startup_epilepsy_review.sh
			Initializes BASH shell >> activates conda environment >> cd to Notebook Dir >> launches Jupyter Lab

	====Configuration Files====		====Configuration Files====
			#Automatically Copied to Analysis folder - Located in $epil_code_path/resources
	default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit		default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit
	processing.cfg : used to preprocess the data for viewing		processing.cfg : used to preprocess the data for viewing

Jstout: /* Add Path */

2019-11-22T22:24:46Z

Add Path

← Older revision		Revision as of 18:24, 22 November 2019
Line 10:		Line 10:
	====Add Path====		====Add Path====
	Use gedit/emacs/vim to add the following lines to the shells path (Either user or system folder)		Use gedit/emacs/vim to add the following lines to the shells path (Either user or system folder)
	#/home/$USER/.bashrc (User folder~~), /etc/profile.d/meg.sh (System Folder - requires sudo - may need to create file meg.sh~~)		#/home/$USER/.bashrc (User folder)
			#/etc/profile.d/meg.sh (System Folder - requires sudo - may need to create file meg.sh)
	export epil_code_path=$path_to_code #This is used in the python code to determine the location of config files in the data		export epil_code_path=$path_to_code #This is used in the python code to determine the location of config files in the data


	====Configuration Files====		====Configuration Files====
	default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit		default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit

Jstout: Code install update

2019-11-22T22:22:56Z

Code install update

@@ Line 2: / Line 2: @@
 After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine
 ====Configuration Files====
   default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit

Jstout at 14:57, 19 November 2019

2019-11-19T14:57:21Z

← Older revision		Revision as of 10:57, 19 November 2019
Line 35:		Line 35:
	====Dipole Fit====		====Dipole Fit====
	Set the time, epoch, and duration of dipole fit		Set the time, epoch, and duration of dipole fit

	Possibly better to set latencies for fits and run through the commandline dipole fit
			Commandline dipole fit
			dfit -a -z -b -0.010 -e 0.010 -h $ds_Filename/default.hdm -f default.dip -m $MarkerName $ds_Filename Output

Jstout at 14:53, 19 November 2019

2019-11-19T14:53:57Z

← Older revision		Revision as of 10:53, 19 November 2019
Line 1:		Line 1:
	UNDER CONSTRUCTION***<br><br><br><br>		UNDER CONSTRUCTION***<br><br><br><br>
	After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine		After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine

			====Configuration Files====
			default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit
			processing.cfg : used to preprocess the data for viewing
			channelset.cfg : Montage Creation (ordering channels is done through virtual channels)
			default.vc : Virtual Channel Creation

	====Configuring Data Editor Layout====		====Configuring Data Editor Layout====
Line 17:		Line 23:

	====Head Model====		====Head Model====
			Preferred Method - Multisphere model from inner skull approximation
			orthohull #Realigns the MRI to match the MEG subject head space (origin is midpoint between LPA/RPA and other axis runs through the nasion)
			#Also creates an inner skull approximation using the inflated/smoothed brain surface
			localSperes -d $Dataset -s multisphere.shape

			Manual Method - Single Shell based on scalp
	MRIConvert >> imports mri into ctf format		MRIConvert >> imports mri into ctf format
	MRIViewer -mri CTF.mri >> creates headshape and headmodel >> save to default.hdm		MRIViewer -mri CTF.mri >> creates headshape and headmodel >> save to default.hdm

Jstout at 19:56, 15 November 2019

2019-11-15T19:56:32Z

← Older revision		Revision as of 15:56, 15 November 2019
Line 21:		Line 21:
	Dipolefit -hdm default.hdm		Dipolefit -hdm default.hdm

			====Dipole Fit====

			Set the time, epoch, and duration of dipole fit
			Possibly better to set latencies for fits and run through the commandline dipole fit

Jstout at 19:55, 15 November 2019

2019-11-15T19:55:04Z

← Older revision		Revision as of 15:55, 15 November 2019
Line 14:		Line 14:
	DataEditor >> Edit >> Virtual Channels		DataEditor >> Edit >> Virtual Channels
	Select a virtual channel and add to Plus Box >> Name the new channel (it must be different from acquisition names - choose lowercase or uppercase as a workaround)		Select a virtual channel and add to Plus Box >> Name the new channel (it must be different from acquisition names - choose lowercase or uppercase as a workaround)
			Save the virtual channel .vg file to $HOME/.meg/resources/default.vg

			====Head Model====
			MRIConvert >> imports mri into ctf format
			MRIViewer -mri CTF.mri >> creates headshape and headmodel >> save to default.hdm
			Dipolefit -hdm default.hdm




			====Processing Pipeline====
			check tags >> cat anat+ortho.HEAD \| grep TAGSET_LABELS
			3dtagalign <<
			avghc.py << creates an average head position
			changeHeadPos << rewrites the head position

Jstout: Created page with "UNDER CONSTRUCTION***

After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine ====Configuring Da..."

2019-11-15T15:45:50Z

Created page with "UNDER CONSTRUCTION*** After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine ====Configuring Da..."

New page

UNDER CONSTRUCTION*** 
After installing and configuring the analysis machine: https://megcore.nih.gov/index.php/Configuring_analysis_machine

====Configuring Data Editor Layout====
Configurations are stored in the ChannelSet.cfg file.
Current Montages Include:
*MEG_LCR_22
*MEG_LCR_22_EEG_LCR_21
*EEG_

====Creating a View Montage====
The data editor layout orders the channels by acquisition order and may not be preferred 
To create ordered channels, a virtual channel dataset will need to be created 
DataEditor >> Edit >> Virtual Channels
Select a virtual channel and add to Plus Box >> Name the new channel (it must be different from acquisition names - choose lowercase or uppercase as a workaround)