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test of h4

tyler
2026-04-22 15:47:38 -07:00
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@@ -127,7 +127,7 @@ If OPTODE_PLACEMENT is set to False, SHOW_OPTODE_NAMES will be ignored.
## Short/Long Channels ## Short/Long Channels
Identifies both short and long channels. A channel is the inter-optode distance between two optodes. Different fNIRS caps will vary in spatial resolution, and as such the requirements for what constitutes a short or long channel will vary depending on the hardware designed and user preferences. If your design has a short channel included, you will need to use this method. If a channel is longer than the allowable distance, it will be removed entirely. If a short channel is requested but no channels are found below the set threshold, the processing of the participant will fail. Identifies both short and long channels. A channel is the inter-optode distance between two optodes. Different fNIRS caps will vary in spatial resolution, and as such the requirements for what constitutes a short or long channel will vary depending on the hardware designed and user preferences. If your design has a short channel included, you will need to use this method. If a channel is longer than the allowable distance, it will be removed entirely. If a short channel is requested but no channels are found below the set threshold, the processing of the participant will fail.
Note: FLARES currently only guarantees support for one short channel. If your design has multiple short channels, raise a feature request on the git page. Note: FLARES currently only guarantees support for one short channel. If your design has multiple short channels, raise a feature request on the git page.
### Parameters #### Parameters
- SHORT_CHANNEL (bool): True if the data has a short channel, False if the data does not have a short channel. - SHORT_CHANNEL (bool): True if the data has a short channel, False if the data does not have a short channel.
- SHORT_CHANNEL_THRESH (float): Maximum distance the short channel can be in metres. - SHORT_CHANNEL_THRESH (float): Maximum distance the short channel can be in metres.
- LONG_CHANNEL_THRESH (float): Maximum distance a channel can be in metres before it is removed. - LONG_CHANNEL_THRESH (float): Maximum distance a channel can be in metres before it is removed.
@@ -198,7 +198,7 @@ Calculates how much a channel varied throughout the experiment. This quality met
If CHANNEL_VAR is set to False, CHANNEL_THRESH will be ignored. If CHANNEL_VAR is set to False, CHANNEL_THRESH will be ignored.
## Bad Channels Handling ## Bad Channels Handling
Determines what to do with channels that were marked as bad in the previous quality steps. There are three options to choose from – “Interpolate”, “Remove”, or “None”. Interpolate will utilize the closest channels to the bad channel and interpolate what the bad channels signal should have been and generate a signal from them. This requires a minimum number of neighbours and the maximum distance a neighbour can be away from the bad channel in metres. If there are not enough neighbours located inside the distance threshold, the offending channel will be unmarked as bad and continue on as if the handling was set to None. Remove will simply drop the channels from memory. None will unflag all the bad channels, and continue as if they are good channels. If bad channels are being removed, an option to completely eliminate a participant is present if they do not meet a specified threshold. Determines what to do with channels that were marked as bad in the previous quality steps. There are three options to choose from - “Interpolate”, “Remove”, or “None”. Interpolate will utilize the closest channels to the bad channel and interpolate what the bad channels signal should have been and generate a signal from them. This requires a minimum number of neighbours and the maximum distance a neighbour can be away from the bad channel in metres. If there are not enough neighbours located inside the distance threshold, the offending channel will be unmarked as bad and continue on as if the handling was set to None. Remove will simply drop the channels from memory. None will unflag all the bad channels, and continue as if they are good channels. If bad channels are being removed, an option to completely eliminate a participant is present if they do not meet a specified threshold.
### Parameters ### Parameters
- BAD_CHANNELS_HANDLING (list): How the bad channels should be dealt with. - BAD_CHANNELS_HANDLING (list): How the bad channels should be dealt with.
- MAX_DIST (float): Maximum distance to look for potential neighbours to interpolate from in meters. - MAX_DIST (float): Maximum distance to look for potential neighbours to interpolate from in meters.
@@ -271,7 +271,7 @@ Uses the previously generated design matrix to make a first level general linear
### Parameters ### Parameters
- NOISE_MODEL (str): Temporal variance model. - NOISE_MODEL (str): Temporal variance model.
- BINS (int): The maximum number of discrete bins for the AR coef. histogram/clustering. - BINS (int): The maximum number of discrete bins for the AR coef. histogram/clustering.
- N_JOBS (int): The number of CPUs to use to do the GLM computation. While -1 signifies ‘all CPUs’, it has been found that limiting this to a single CPU ends up being faster on higher end devices. - N_JOBS (int): The number of CPUs to use to do the GLM computation. While -1 signifies 'all CPUs', it has been found that limiting this to a single CPU ends up being faster on higher end devices.
## Finishing Touches ## Finishing Touches
This stage just involves some under-the-hood calculations that will be used for further analysis. This process is self contained and is required step, so it does not contain any user exposed parameters. This stage just involves some under-the-hood calculations that will be used for further analysis. This process is self contained and is required step, so it does not contain any user exposed parameters.
## Other ## Other