Difference between revisions of "Configuring Epilepsy Analysis"

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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
  +
  +
====Configuration Files====
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default.dip : used as input to the dipoleFit and dfit programs as the default starting options for dipole fit
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processing.cfg : used to preprocess the data for viewing
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channelset.cfg : Montage Creation (ordering channels is done through virtual channels)
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default.vc : Virtual Channel Creation
   
 
====Configuring Data Editor Layout====
 
====Configuring Data Editor Layout====
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====Head Model====
 
====Head Model====
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Preferred Method - Multisphere model from inner skull approximation
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orthohull #Realigns the MRI to match the MEG subject head space (origin is midpoint between LPA/RPA and other axis runs through the nasion)
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#Also creates an inner skull approximation using the inflated/smoothed brain surface
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localSperes -d $Dataset -s multisphere.shape
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  +
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

Revision as of 10:53, 19 November 2019

UNDER CONSTRUCTION***



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

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
 Possibly better to set latencies for fits and run through the commandline dipole fit


Processing Pipeline

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