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 area files
  • AAL-area file (_aal.area.mat) : AAL maps
  • Destrieux-area file (_Destrieux.area.mat) : freesurfer(.aparc.a2009s.annot)
  • Desikan-Killany-area file (_Desikan-Killany.area.mat) : freesurfer(.aparc.annot)
  • Yeo2011_7Networks-area file (_Yeo2011_7Networks.area.mat) : freesurfer(.Yeo2011_7Networks_N1000.annot)
  • Yeo2011_17Networks-area file (_Yeo2011_17Networks.area.mat) : freesurfer(.Yeo2011_17Networks_N1000.annot)

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

• MEG
  • Yokogawa
  • Neuromag (Neuromag toolbox)
• EEG
  • Biosemi
  • BrainAmp

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

• M/EEG Standard-format document(refer to Minimum format)

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.