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HDDOT

Transform fNIRS optical densities into brain mesh images using optical tomography.

This can use a pre-computed Jacobian that is matched to a specific NIRS montage or it will re-compute the Jacobian using toast++ finite element solver to simulate light propagation through the head, and then uses the inverse model to calculate magnitudes at the cortical surface. Version 0.3.1

Ports/Properties

data

Data to process.

verbose name
Data
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
INOUT

headmodel

Head model file to use (.h m or .mshs). If omitted, the node checks if the data has a current head model associated with it, e.g., because a previous node has annotated it, and then uses that head model. If a relative path is given, the file is searched in the resources/headmodels folder of the cpe.

verbose name
Head Model File
default value
port type
StringPort
value type
str (can be None)

save_jacobian_path

Path (including filename) to save computed Jacobian.

verbose name
Save Jacobian Path
default value
port type
StringPort
value type
str (can be None)

load_jacobian_path

Path (including filename) to an existing Jacobian file if available. If file doesn't exist or isn't compatible it will be recomputed

verbose name
Load Jacobian Path
default value
port type
StringPort
value type
str (can be None)

basis

Dimensions of mesh rasterization grid. Maps between the unstructured FEM and a regular pixel/voxel grid used for reconstruction.

verbose name
Basis
default value
[30, 30, 30]
port type
ListPort
value type
list (can be None)

fine_basis

Dimensions of intermediate mesh rasterization grid.

verbose name
Fine Basis
default value
[60, 60, 60]
port type
ListPort
value type
list (can be None)

refraction_index

Always 1.3 in DOTHUB

verbose name
Refraction Index
default value
1.3
port type
FloatPort
value type
float (can be None)

jtype

Solver to use.

verbose name
Jtype
default value
bicgstab
port type
EnumPort
value type
str (can be None)

jtol

Convergence tolerance

verbose name
Jtol
default value
1e-12
port type
FloatPort
value type
float (can be None)

regularizer_params

Regularization proportion.

verbose name
Regularizer Params
default value
[0.01]
port type
ListPort
value type
list (can be None)

channel_pattern

Channel pattern naming using a regex pattern. This is a search pattern used to associate source and detector pairs along with their respective wavelength value. Regex pattern must include '' for the source IDs and '' for the detector IDs, '' can optionally be used for wavelength value if that is specified in the channel names, otherwise if '' is excluded in the regex pattern it will require wavelength values are stored in the space axis 'units' array with the same length as the number of channel names. Default regex pattern expects channel names in format example 'S01-D02-680' (e.g. Source ID#1 connected to Detector ID#2 with wavelength 680 nm.

verbose name
Channel Pattern
default value
S(?P<src>\d*)-D(?P<dct>\d*)-(?P<wl>\d*)
port type
StringPort
value type
str (can be None)

set_breakpoint

Set a breakpoint on this node. If this is enabled, your debugger (if one is attached) will trigger a breakpoint.

verbose name
Set Breakpoint (Debug Only)
default value
False
port type
BoolPort
value type
bool (can be None)

metadata

User-definable meta-data associated with the node. Usually reserved for technical purposes.

verbose name
Metadata
default value
{}
port type
DictPort
value type
dict (can be None)