Configuring Epilepsy Analysis: Difference between revisions

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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

====Download Code for Epilepsy Analysis====
git clone $USER@$GIT_SERVER:epilepsy

#Once installed, go into the code folder and to update
git pull

====Add Path====
Use gedit/emacs/vim to add the following lines to the shells path (Either user or system folder)
#/home/$USER/.bashrc (User folder)
#/etc/profile.d/meg.sh (System Folder - requires sudo - may need to create file meg.sh)
export epil_code_path=$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
#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====
#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
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====
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====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
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====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




Latest revision as of 19:20, 26 November 2019

UNDER CONSTRUCTION***



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

Download Code for Epilepsy Analysis

 git clone  $USER@$GIT_SERVER:epilepsy

 #Once installed, go into the code folder and to update
 git pull

Add Path

 Use gedit/emacs/vim to add the following lines to the shells path (Either user or system folder)
 #/home/$USER/.bashrc  (User folder)
 #/etc/profile.d/meg.sh  (System Folder - requires sudo - may need to create file meg.sh)
 export epil_code_path=$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
 #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

 #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
 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

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)
 Save the virtual channel .vg file to $HOME/.meg/resources/default.vg

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
 MRIViewer -mri CTF.mri >> creates headshape and headmodel >> save to default.hdm
 Dipolefit -hdm default.hdm

Dipole Fit

 Set the time, epoch, and duration of 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


Processing Pipeline

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

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