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Develop
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@arioskyag
arioskyag authored Dec 1, 2023
2 parents 7d7f6ba + 4cbfe52 commit 225317f
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84 changes: 43 additions & 41 deletions README.md
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Expand Up @@ -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=<<openmeeg>> MEG=<<os_meg>>. Others options <<meg_sphere>> <<eeg_3sphereberg>> <<duneuro>>
- 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 --> <<iso2mesh>> <<brain2mesh>> <<simnibs>> <<roast>> <<fieldtrip>>
- value --> Default:iso2mesh
- MeshType --> iso2mesh=<<tetrahedral>>. simnibs=<<tetrahedral>>. roast=<<hexahedral>>|<<tetrahedral>>. fieldtrip=<<hexahedral>>|<<tetrahedral>>
- 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 <<mergemesh>>|<<mergesurf>> 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 --> <<iso2mesh>> <<brain2mesh>> <<simnibs>> <<roast>> <<fieldtrip>>
- value --> Default:iso2mesh
- MeshType --> iso2mesh=<<tetrahedral>>. simnibs=<<tetrahedral>>. roast=<<hexahedral>>|<<tetrahedral>>. fieldtrip=<<hexahedral>>|<<tetrahedral>>
- 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 <<mergemesh>>|<<mergesurf>> 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
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206 changes: 103 additions & 103 deletions cfs_properties/defaults/process_comp_headmodel.json
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Expand Up @@ -2,114 +2,114 @@
"description":"",
"Method":{
"description":"Recommended options EEG=<<openmeeg>> MEG=<<os_meg>>. Others options <<meg_sphere>> <<eeg_3sphereberg>> <<duneuro>> ",
"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":"<<iso2mesh-2021>> <<iso2mesh>> <<brain2mesh>> <<simnibs3>> <<simnibs4>> <<fieldtrip>>",
"value":"iso2mesh-2021"
},
"Methods":[
{
"name":"iso2mesh-2021",
"MergeMethod":{
"description":"iso2mesh <<mergemesh>>|<<mergesurf>> 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":"<<iso2mesh-2021>> <<iso2mesh>> <<brain2mesh>> <<simnibs3>> <<simnibs4>> <<fieldtrip>>",
"value":"iso2mesh-2021"
},
{
"name":"iso2mesh",
"MergeMethod":{
"description":"iso2mesh <<mergemesh>>|<<mergesurf>> Function used to merge the meshes",
"value":"mergesurf"
"Methods":[
{
"name":"iso2mesh-2021",
"MergeMethod":{
"description":"iso2mesh <<mergemesh>>|<<mergesurf>> 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 <<mergemesh>>|<<mergesurf>> 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
}
}
}
]
]
}
}
}
]
]
}
}
14 changes: 7 additions & 7 deletions cfs_properties/defaults/process_import_anat.json
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@@ -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. <<template>> Brainstorm default anatomy. <<individual>> HCP individual anatomy",
"type":"individual",
"type_list":[
{
"id":1,
"id":"default",
"name":"default_anatomy",
"description":"Select the group and name of the sensor layout. See app/bst_default_anatomy.json file and select all params from there",
"template_name":"ICBM152_2023",
"template_name":"ICBM152_2023b",
"default_atlas":"Desikan-Killiany"
},
{
"id":2,
"id":"individual",
"name":"hcp_anat_individual",
"description":"",
"base_path":"/mnt/Store/Data/CHBM/Test/Ciftify",
Expand All @@ -33,11 +33,11 @@
},
"layer_desc":{
"description":"Layer descriptor. Options <<white>> OR <<midthickness>> OR <<pial>> OR <<bigbrain>> multilayer like bigbrain OR <<fs_LR>> like HCP FSAve (three layers).",
"desc":"midthickness"
"desc":"Midthickness"
},
"surfaces_resolution":{
"description":"Numbers of vertices for downsample the surfaces: default <<8000>>",
"nvertices":8000
}
}
}
}
12 changes: 6 additions & 6 deletions cfs_properties/defaults/process_import_channel.json
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@@ -1,28 +1,28 @@
{
"description":"",
"channel_type":{
"description":"Select the type of import channel process to be used. <<1>> Use raw data. <<2>> Use BST default template ",
"type":2,
"description":"Select the type of import channel process to be used. <<raw>> Use raw data. <<default>> Use BST default template ",
"type":"default",
"type_list":[
{
"id":1,
"id":"raw",
"name":"raw_data",
"description":"",
"subID_prefix":"",
"base_path":"/mnt/Store/Data/Conectome/Sample/SubID",
"base_path":"/mnt/Store/Data/Conectome/Sample",
"file_location":"meg/SubID/unprocessed/MEG/5-Restin/4D/c,rfDC",
"data_format":"4D",
"group_layout_name":"",
"channel_layout_name":""
},
{
"id":2,
"id":"default",
"name":"import_channel",
"description":"Select the group and name of the sensor layout. See bst_defaults/bst_eeg_layouts.json file and select all params from there",
"group_layout_name":"ICBM152",
"channel_layout_name":"ASA 10-05 343"
}
]
},
"channel_label_file":""
"channel_label_file":""
}
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