vbmeg2_job_functions

vb_job_brain

Description

Convert FreeSurfer data to VBMEG format.

Syntax

vb_job_brain(proj_root,brain_parm)

Output files

  • VBMEG Cortical model file (.brain.mat)
  • VBMEG Cortical act file (.act.mat)
  • VBMEG Cortical area file (.area.mat)

For anatomical area display.

  • VBMEG Cortical AAL-area file (_aal.area.mat) : AAL maps
  • VBMEG Cortical Brodmann-area file (_aal.brodmann.area.mat) : Brodmann maps

Parameters

proj_root
VBMEG project root directory.
brain_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_brain_parm.
.analyze_file
<<string>> MRI filename (.nii/.hdr)
.FS_left_file
<<string>> FreeSurfer left smooth white matter file.
.FS_right_file
<<string>> FreeSufer right smooth white matter file.
.FS_left_infl_file
<<string>> FreeSurfer left inflate model file.
.FS_right_infl_file
<<string>> FreeSurfer right inflate model file.
.FS_left_curv_file
<<string>> FreeSurfer left curvature file.
.FS_right_curv_file
<<string>> FreeSurfer right curvature file.
.FS_left_label_file
<<string>> FreeSurfer left label file.
.FS_right_label_file
<<string>>FreeSurfer right label file.
.FS_left_sphere_file
<<string>>FreeSurfer left sphere file.
.FS_right_sphere_file
<<string>> FreeSurfer right sphere file.
.brain_file
<<string>> Cortical surface model file (.brain.mat).
.act_file
<<string>> Cortical activity map file (.act.mat).
.area_file
<<string>>Cortical area file (.area.mat).

Remarks : Describe brain_file, act_file, area_file in a relative path from proj_root.

vb_job_head_3shell

Description

Make 1-shell(CSF) for MEG or 3-shell(CSF, Skull, Scalp) surface model for EEG.

syntax

vb_job_head_3shell(proj_root, head_parm)

Output file

  • VBMEG Head model file (.head.mat)

Parameters

proj_root
VBMEG project root directory.
head_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_head_parm.
.analyze_file
<<string>> MRI filename (.nii/.hdr)
.fs_scalp_file
<<string>> FreeSurfer outer skin surface file.
.gray_file
<<string>> Gray matter file created by SPM8 Segment function(='c1**.nii/.hdr');
.freesurf_file
<<string>> FreeSurfer inner skull surface file.
.brain_file
<<string>> Cortical surface model file (.brain.mat).
.Nsurf
<<integer>> Head model type
=1:CSF model(for MEG)
=3:3shell model(for EEG)
.Nvertex
<<integer>> The number of vertices of each head tissue model.
.head_file
<<string>> Head model file(.head.mat)

Remarks : Describe brain_file, head_file in a relative path from proj_root.

vb_job_fmri

Description

Import fMRI activities as a prior information.

Syntax

vb_job_fmri(proj_root, fmri_parm)

Update files

  • VBMEG Cortical act file (.act.mat) : fMRI activity (T value, PS value) is saved.
  • VBMEG Cortical area file (.area.mat) : The location where the fMRI activity exists is saved.

Parameters

proj_root
VBMEG project root directory.
fmri_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_fmri_parm.
.SPMmat_file
<<string>> SPM result file(SPM.mat)
.SPMmapmode
<<string>> SPM result map mode(fMRI coordinate to VBMEG Cortical model).
= 'mni2mni' : SPM analysis was conducted on the MNI template brain model.
.keys_postfix
<<string>> postfix of keys of fmri activity that will be stored to VBMEG act and area files.
.Tthres
<<real>> T-value threshold(one-sided) (no unit)
.PSthres
<<real>> Parcent signal change threshold(two-sided) (unit: %s)
.Rthres
<<real>> Radius threshold for converting a voxel image to a surface image(unit:mm)
.brain_file
<<string>> Cortical surface model file (.brain.mat).
.act_file
<<string>> Cortical activity map file (.act.mat).
.area_file
<<string>>Cortical area file (.area.mat).

Remarks : Describe brain_file, act_file, area_file in a relative path from proj_root.

vb_job_meg

Description

Import M/EEG data and create VBMEG MEG (.meg.mat) or EEG (.eeg.mat) file.
Supported measurement data are

If this function is not compatible with your device, you can create a file with reference to this document.

Syntax

vb_job_meg(proj_root, meg_parm)

Output file

  • VBMEG MEG-MAT file (.meg.mat) or VBMEG EEG-MAT file (.eeg.mat)

Parameters for Yokogawa MEG

proj_root
VBMEG project root directory.
meg_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_yokogawa_meg_parm.
.Measurement
<<string>> hardware type (set 'MEG').
.device
<<string>> device type (set 'YOKOGAWA').
.yokogawa_file
<<string>> Yokogawa MEG file(.con/.raw/.ave).
.pos_file
<<string>> sensor location file(.pos.mat).
This is made by positioning program.
.meg_file
<<string>> VBMEG MEG file (.meg.mat)

Remarks : Describe meg_file in a relative path from proj_root.

Parameters for Biosemi EEG

proj_root
VBMEG project root directory.
meg_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_meg_parm_brainamp.
.Measurement
<<string>> hardware type (set to 'EEG').
.device
<<string>> device type(set to 'BIOSEMI').
.measurement_file
<<string>> Biosemi EEG file(.bdf).
.pos_file
<<string>> sensor location file(.pos.mat).
This is made by positioning program.
.output_file
<<string>> VBMEG EEG file (.eeg.mat).

Remarks : Describe output_file in a relative path from proj_root.

Parameters for BrainAmp

meg_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_meg_parm_brainamp.
.Measurement
<<string>> hardware type (set to 'EEG').
.device
<<string>> device type(set to 'BRAINAMP').
.measurement_file
<<string>> BrainAmp EEG file(.eeg).
.pos_file
<<string>> sensor location file(.pos.mat).
This is made by positioning program.
.output_file
<<string>> VBMEG EEG file (.eeg.mat).

Remarks : Describe output_file in a relative path from proj_root.

vb_job_leadfield

Description

Calculate leadfield matrix for using the following numerical methods:

  • MEG Sphere model (Sarvas equation)
  • MEG 1-shell BEM (boundary element method)
  • MEG Spherical harmonics expansion
  • EEG 3-shell Sphere model
  • EEG 3-shell BEM

Syntax

vb_job_leadfield(proj_root, basis_parm)

Output file

  • VBMEG Leadfield file (.basis.mat)

Parameters

proj_root
VBMEG project root directory.
basis_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_basis_parm.
.brain_file
<<string>> Cortical surface model file (.brain.mat).
.meg_file
<<string>> VBMEG MEG/EEG file (.meg.mat/.eeg.mat).
.bem_mode
<<integer>> calculation methods.
0:MEG Sphere model (Sarvas)
1:MEG 1-shell BEM
2:MEG Spherical harmonics expansion
3:EEG 3-shell Sphere model
4:EEG 3-shell BEM
.head_file
<<string>> (optional) VBMEG head model file (.head.mat). This is used for BEM method.
.basis_file
<<string>> VBMEG leadfield file (.basis.mat)

Remarks : Describe brain_file, meg_file, head_file, basis_file in a relative path from proj_root.

vb_job_vb

Description

Compute current variance from the M/EEG data using Hierarchical bayesian method.

Syntax

vb_job_vb(proj_root, bayes_parm)

Output file

  • VBMEG Current variance file (.bayes.mat)

Parameters

proj_root
VBMEG project root directory.
bayes_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_bayes_default_parameters.
.brainfile
<<string>> Cortical surface model file (.brain.mat).
.reduce
<<real>> Parameter for spatially uniformly thinning the number of vertices of the brain model. 0.1 corresponds to setting the number of vertices to 1/10.
.Rfilt
<<real>> Smoothing filter radius in [m]
.basisfile
<<string>> VBMEG leadfield file (.basis.mat)
.areafile
<<string>> VBMEG Cortical area file (.area.mat).
.area_key
<<string>> The key for specifying the area to assume the current source.
.actfile
<<string>> VBMEG Cortical activity file (.act.mat).
.act_key
<<string>> A key to specify which fMRI strength information of the activity contained in actfile to use as prior information.
.prior_weight
<<real>> Relative influence of prior information on data(from 0 to 1 real).
.a0_act
<<real>> Maximum value of current variance parameter.
.megfile
<<string or cell string>> VBMEG MEG/EEG file (.meg.mat/.eeg.mat).
.twin_meg
<<vector>> Analysis time range(twin_meg = [from, to])(unit:sample). from, to is the sample number of the data specified in bayes_parm.meg_file.
.Tnext
<<integer>> Partial time window length of MEG data(unit:sample).
.Tperiod
<<integer>> Moving step length of partial time of MEG data(unit:sample).
.twin_noise
<<vector>> Observation noise covariance matrix is calculated using MEG data bayes_parm.megfile within this time window, specified by start and end.
.twin_baseline
<<vector>> Baseline observation noise variance (rho_{base}) and baseline current variance parameter (nu_{0,base}) are estimated from MEG data within the time window, specified by start and end.
.Npre_train
<<integer>> Iteration number of fast VB algorithm.
.Ntrain
<<integer>> Iteration number of VB algorithm.
.skip
<<integer>> Calculate free energy at each skip steps.
.trial_average
<<integer>> If true, trial average is applied to the MEG data.
.patch_norm
<<bool>> If true, patch area normalization is applied. That is, dipole current moment (Am) is replaced by its (area) density (Am/m^2).
.noise_reg
<<real>> Regularization parameter for observarion noise covariance matrix. This value is used to suppress singularity of the covariance matrix.
.bayesfile
<<string>> VBMEG Current variance file (.bayes.mat).

Remarks : Describe brainfile, areafile, actfile, megfile, bayesfile in a relative path from proj_root.

vb_job_current

Description

Calculate cortical current from the estimated current variance and M/EEG data.

Syntax

vb_job_current(proj_root, current_parm)

Output file(s)

  • VBMEG Cortical current file (.curr.mat)

    (if you specify current_parm.jactdir, the estimated current for each trial is saved for each file under the specified directory.)

Parameters

proj_root
VBMEG project root directory.
current_parm
<<structure>> The fields are as below. In order to get the default parameters, execute vb_set_current_parm.
.bayesfile
<<string>> VBMEG Current variance file (.bayes.mat).
.trial_average
<<integer>>
0:Calculate current for each trial.
1:Calculate current over all trials.
.currfile
<<string>> VBMEG Cortical current file (.curr.mat)
.jactdir
<<string>> (optional) If current for each trial is calculated (trial_average = OFF), data size exceed the maximum memory or file size limit, specify this output directory, then save current file for each trial.

Remarks : Describe bayesfile, currfile in a relative path from proj_root.