diff --git a/README.md b/README.md index 488d4be..5e17eac 100644 --- a/README.md +++ b/README.md @@ -63,49 +63,51 @@ A pipeline to integrate “legacy” datasets into a Human Connectome Project (H - channel_layout_name --> ## Compute Headmodel process [[File]](https://github.com/CCC-members/CiftiStorm/blob/master/cfs_properties/process_comp_headmodel.json) -### Default parameter configuration - - radii --> Default: [0.88,0.93,1] - - conductivity --> Default: [0.33,0.0042,0.33] - - BemNames --> Default: ["Scalp","Skull","Brain"] - - BemCond --> Default: [1,0.0125,1] - - BemSelect --> Default: [true,true,true] +### Default parameter configuration - Method --> Recommended options EEG=<> MEG=<>. Others options <> <> <> - value --> - - method_type --> - - openmeeg - - EEGMethod --> - - isAdjoint --> - - isAdaptative --> - - isSplit --> - - SplitLength --> - - os_meg - - MEGMethod --> - - duneuro - - FemCond --> Default: [1.79,0.0080,0.43] - - FemSelect --> Default: [1,1,1] - - Isotropic --> Default: 1 - - UseTensor --> Default: 0 - - FemMesh --> - - Method --> <> <> <> <> <> - - value --> Default:iso2mesh - - MeshType --> iso2mesh=<>. simnibs=<>. roast=<>|<>. fieldtrip=<>|<> - - value --> Default: tetrahedral - - MaxVol --> iso2mesh Max tetrahedral volume (10=coarse, 0.0001=fine) - - value --> Default: 0.1 - - KeepRatio --> iso2mesh Percentage of elements kept (1-100%) - - value --> Default: 100 - - MergeMethod --> iso2mesh <>|<> Function used to merge the meshes - - value --> Default: mergesurf - - VertexDensity--> SimNIBS <<0.1 - X>> setting the vertex density (nodes per mm2) of the surface meshes - - value --> Default: 0.5 - - NbVertices --> SimNIBS Number of vertices for the cortex surface imported from CAT12 - - value --> Default: 15000 - - NodeShift --> FieldTrip <<0 - 0.49>> Improves the geometrical properties of the mesh - - value --> Default: 0.3 - - Downsample --> FieldTrip Integer, Downsampling factor to apply to the volumes before meshing - - value --> Default: 3 - - Zneck --> Input T1/T2: Cut volumes below neck (MNI Z-coordinate) - - value --> Default: -115 + - methods --> + - meg_sphere + - MEGMethod --> + - os_meg + - MEGMethod --> + - eeg_3sphereberg + - EEGMethod --> + - openmeeg + - BemNames --> Default: ["Scalp","Skull","Brain"] + - BemCond --> Default: [1,0.0125,1] + - BemSelect --> Default: [true,true,true] + - EEGMethod --> + - isAdjoint --> + - isAdaptative --> + - isSplit --> + - SplitLength --> + - duneuro + - FemCond --> Default: [1.79,0.0080,0.43] + - FemSelect --> Default: [1,1,1] + - Isotropic --> Default: 1 + - UseTensor --> Default: 0 + - FemMesh --> + - Method --> <> <> <> <> <> + - value --> Default:iso2mesh + - MeshType --> iso2mesh=<>. simnibs=<>. roast=<>|<>. fieldtrip=<>|<> + - value --> Default: tetrahedral + - MaxVol --> iso2mesh Max tetrahedral volume (10=coarse, 0.0001=fine) + - value --> Default: 0.1 + - KeepRatio --> iso2mesh Percentage of elements kept (1-100%) + - value --> Default: 100 + - MergeMethod --> iso2mesh <>|<> Function used to merge the meshes + - value --> Default: mergesurf + - VertexDensity--> SimNIBS <<0.1 - X>> setting the vertex density (nodes per mm2) of the surface meshes + - value --> Default: 0.5 + - NbVertices --> SimNIBS Number of vertices for the cortex surface imported from CAT12 + - value --> Default: 15000 + - NodeShift --> FieldTrip <<0 - 0.49>> Improves the geometrical properties of the mesh + - value --> Default: 0.3 + - Downsample --> FieldTrip Integer, Downsampling factor to apply to the volumes before meshing + - value --> Default: 3 + - Zneck --> Input T1/T2: Cut volumes below neck (MNI Z-coordinate) + - value --> Default: -115 ## Run CiftiStorm * Open CiftiStorm pipeline on Matlab diff --git a/cfs_properties/defaults/process_comp_headmodel.json b/cfs_properties/defaults/process_comp_headmodel.json index 6301245..bbb4997 100644 --- a/cfs_properties/defaults/process_comp_headmodel.json +++ b/cfs_properties/defaults/process_comp_headmodel.json @@ -2,114 +2,114 @@ "description":"", "Method":{ "description":"Recommended options EEG=<> MEG=<>. Others options <> <> <> ", - "value":"openmeeg" - }, - "method_type":[ - { - "name":"meg_sphere", - "description":"", - "MEGMethod":"meg_sphere" - }, - { - "name":"os_meg", - "description":"", - "MEGMethod":"os_meg" - }, - { - "name":"eeg_3sphereberg", - "description":"", - "EEGMethod":"eeg_3sphereberg" - }, - { - "name":"openmeeg", - "description":"", - "EEGMethod":"openmeeg", - "BemNames":["Scalp","Skull","Brain"], - "BemCond":[1,0.0125,1], - "BemSelect":[true,true,true], - "isAdjoint":false, - "isAdaptative":true, - "isSplit":false, - "SplitLength":4000 - }, - { - "name":"duneuro", - "description":"", - "EEGMethod":"duneuro", - "FemCond":[1.79,0.008,0.43], - "FemSelect":[true,true,true], - "Isotropic":true, - "UseTensor":false, - "FemMesh":{ - "Method":{ - "description":"<> <> <> <> <> <>", - "value":"iso2mesh-2021" - }, - "Methods":[ - { - "name":"iso2mesh-2021", - "MergeMethod":{ - "description":"iso2mesh <>|<> Function used to merge the meshes", - "value":"mergesurf" - }, - "MaxVol":{ - "description":"Default <<0.1>>. iso2mesh Max tetrahedral volume (10=coarse - 0.0001=fine)", - "value":0.1 - }, - "KeepRatio":{ - "description":"Default <<100>>. iso2mesh Percentage of elements kept (1-100%)", - "value":100 - } + "value":"openmeeg", + "methods":[ + { + "name":"meg_sphere", + "description":"", + "MEGMethod":"meg_sphere" + }, + { + "name":"os_meg", + "description":"", + "MEGMethod":"os_meg" + }, + { + "name":"eeg_3sphereberg", + "description":"", + "EEGMethod":"eeg_3sphereberg" + }, + { + "name":"openmeeg", + "description":"", + "EEGMethod":"openmeeg", + "BemNames":["Scalp","Skull","Brain"], + "BemCond":[1,0.0125,1], + "BemSelect":[true,true,true], + "isAdjoint":false, + "isAdaptative":true, + "isSplit":false, + "SplitLength":4000 + }, + { + "name":"duneuro", + "description":"", + "EEGMethod":"duneuro", + "FemCond":[1.79,0.008,0.43], + "FemSelect":[true,true,true], + "Isotropic":true, + "UseTensor":false, + "FemMesh":{ + "Method":{ + "description":"<> <> <> <> <> <>", + "value":"iso2mesh-2021" }, - { - "name":"iso2mesh", - "MergeMethod":{ - "description":"iso2mesh <>|<> Function used to merge the meshes", - "value":"mergesurf" + "Methods":[ + { + "name":"iso2mesh-2021", + "MergeMethod":{ + "description":"iso2mesh <>|<> Function used to merge the meshes", + "value":"mergesurf" + }, + "MaxVol":{ + "description":"Default <<0.1>>. iso2mesh Max tetrahedral volume (10=coarse - 0.0001=fine)", + "value":0.1 + }, + "KeepRatio":{ + "description":"Default <<100>>. iso2mesh Percentage of elements kept (1-100%)", + "value":100 + } }, - "MaxVol":{ - "description":"Default <<0.1>>. iso2mesh Max tetrahedral volume (10=coarse - 0.0001=fine)", - "value":0.1 + { + "name":"iso2mesh", + "MergeMethod":{ + "description":"iso2mesh <>|<> Function used to merge the meshes", + "value":"mergesurf" + }, + "MaxVol":{ + "description":"Default <<0.1>>. iso2mesh Max tetrahedral volume (10=coarse - 0.0001=fine)", + "value":0.1 + }, + "KeepRatio":{ + "description":"Default <<100>>. iso2mesh Percentage of elements kept (1-100%)", + "value":100 + } }, - "KeepRatio":{ - "description":"Default <<100>>. iso2mesh Percentage of elements kept (1-100%)", - "value":100 - } - }, - { - "name":"brain2mesh" - }, - { - "name":"simnibs3", - "VertexDensity":{ - "description":"SimNIBS <<0.1 - X>> setting the vertex density (nodes per mm2) of the surface meshes", - "value":0.5 + { + "name":"brain2mesh" }, - "NbVertices":{ - "description":"SimNIBS Number of vertices for the cortex surface imported from CAT12", - "value":15000 - } - }, - { - "name":"simnibs4", - "NbVertices":{ - "description":"SimNIBS Number of vertices for the cortex surface imported from CAT12", - "value":15000 - } - }, - { - "name":"fieldtrip", - "Downsample":{ - "description":"FieldTrip Integer, Downsampling factor to apply to the volumes before meshing", - "value":3 + { + "name":"simnibs3", + "VertexDensity":{ + "description":"SimNIBS <<0.1 - X>> setting the vertex density (nodes per mm2) of the surface meshes", + "value":0.5 + }, + "NbVertices":{ + "description":"SimNIBS Number of vertices for the cortex surface imported from CAT12", + "value":15000 + } + }, + { + "name":"simnibs4", + "NbVertices":{ + "description":"SimNIBS Number of vertices for the cortex surface imported from CAT12", + "value":15000 + } }, - "NodeShift":{ - "description":"FieldTrip <<0 - 0.49>> Improves the geometrical properties of the mesh", - "value":0.3 + { + "name":"fieldtrip", + "Downsample":{ + "description":"FieldTrip Integer, Downsampling factor to apply to the volumes before meshing", + "value":3 + }, + "NodeShift":{ + "description":"FieldTrip <<0 - 0.49>> Improves the geometrical properties of the mesh", + "value":0.3 + } } - } - ] + ] + } } - } - ] + ] + } } \ No newline at end of file diff --git a/cfs_properties/defaults/process_import_anat.json b/cfs_properties/defaults/process_import_anat.json index affd7cd..dc989e8 100644 --- a/cfs_properties/defaults/process_import_anat.json +++ b/cfs_properties/defaults/process_import_anat.json @@ -1,18 +1,18 @@ { "description":"", "anatomy_type":{ - "description":"Select the type of anatomy to use. <<1>> Brainstorm default anatomy. <<2>> HCP anatomy as Template <<3>> HCP individual anatomy", - "type":2, + "description":"Select the type of anatomy to use. <