Create vol and leadfield from individual MRI using Fieldtrip
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README
bash.m
bnd2lead.m
cpmri.m
freesurfer2bnd.m
license
mri2bnd.m
smudge.m
usetemplate.m

README

Create vol and leadfield based on individual MRIs using Fieldtrip

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MAIN FUNCTIONS
- CPMRI: copy MRI images into subject-folder and normalize them
- MRI2BND: create mesh based on MRI using fieldtrip segmentation
- FREESURFER2BND: create mesh based on MRI using freesurfer
- BND2LEAD: create leadfield
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INFO
.data: path of /data1/projects/PROJ/subjects/
  CPMRI, MRI2BND, FREESURFER2BND, BND2LEAD, 
  
.log: name of the file and directory to save log
  CPMRI, MRI2BND, FREESURFER2BND, BND2LEAD, 
  
.smri: folder containing all the MRI images
  CPMRI, 
  
.rec: REC in /data1/projects/PROJ/recordings/REC/
  CPMRI, MRI2BND, FREESURFER2BND, BND2LEAD, 

.recs: name of recordings/RECNAME/subjects/
  CPMRI, 
  
.sens.file: file with EEG sensors. It can be sfp or mat.
  BND2LEAD,
  
.sourcespace: 'surface' or 'volume' or 'volume_warp'
  BND2LEAD
  
.vol.cond: name to be used in projects/PROJNAME/subjects/0001/VOLMOD/VOLCONDNAME/
  CPMRI, MRI2BND, FREESURFER2BND, BND2LEAD, 
  
.vol.mod: name to be used in projects/PROJNAME/subjects/0001/VOLMOD/
  CPMRI, MRI2BND, FREESURFER2BND, BND2LEAD, 
  
.vol.type: bem-model ('dipoli' or 'openmeeg')
  BND2LEAD, 
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CFG.OPT

.brain.smooth: smoothing kernel for brain (5 cm)
  MRI2BND, 

.brain.threshold: threshold of tpm for brain (0.5)
  MRI2BND, 

.brain.numvertices: # vertices for brain (2500)
  MRI2BND, 
  
.conductivity: conductivity of tissues ([0.3300 0.0042 0.3300])
  BND2LEAD,  
  
.elecM: 4x4 affine matrix of the transformation of the electrodes
  BND2LEAD, 

.mni.nonlinear (if 'volume_warp')*: run non-linear mni registration ('yes' or 'no')
  BND2LEAD,  
  
.mni.resolution (if 'volume_warp')*: resolution of the grid (5,6,8,10 mm)
  BND2LEAD,  

.normalize: normalization ('none' 'spm8' 'flirt')
  CPMRI, MRI2BND, 

.reducesurf: ratio to reducepatch of surface (1 -> intact, .5 -> half)
  FREESURFER2BND,

.reducegrid: ratio to reducepatch of source grid (1 -> intact, .5 -> half)
  FREESURFER2BND,
  
.scalp.smooth: smoothing kernel for scalp (5 cm)
  MRI2BND, 

.scalp.threshold: threshold of tpm for scalp (0.1)
  MRI2BND, 

.scalp.numvertices: # vertices for scalp (2500)
  MRI2BND, 

.skull.smooth: smoothing kernel for skull (5 cm)
  MRI2BND, 

.skull.threshold: threshold of tpm for skull (0.5)
  MRI2BND, 

.skull.numvertices: # vertices for skull (2500)
  MRI2BND, 

.smudgeiter: iteration for smudging (default = 6) (it's possible to rerun this function, only to change the amount of smudging)
  FREESURFER2BND,
  
.SUBJECTS_DIR: where the Freesurfer data is stored (like the environmental variable), with extra slash 
  FREESURFER2BND,

.surftype: name of the surface to read ('smoothwm' 'pial' 'white' 'inflated' 'orig' 'sphere')  
  FREESURFER2BND,
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