From 91b5865dc0fe73b856c20c05005b89f7f0e8a6b9 Mon Sep 17 00:00:00 2001 From: tyler Date: Thu, 10 Sep 2026 11:50:20 -0700 Subject: [PATCH] Update Understanding Parameters --- Understanding-Parameters.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Understanding-Parameters.md b/Understanding-Parameters.md index d7eb136..2d8253a 100644 --- a/Understanding-Parameters.md +++ b/Understanding-Parameters.md @@ -2,15 +2,15 @@ This page is dedicated to understanding the parameters inside the Parameter section on the right of the screen. If you haven't already, visit the [Home Page](https://git.research.dezeeuw.ca/tyler/flares/wiki/Home) before following along with this guide. -All parameters discussed in this Wiki page are global parameters. This means that every snirf file loaded will have the same parameters applied to them. If you think a parameter should be on a per file basis (such as Age, Gender, Group) and not on a global basis, raise a [feature request](https://git.research.dezeeuw.ca/tyler/flares/issues/new) along with an explaination as to why you think it should be on a per file basis. +All parameters discussed in this Wiki page are global parameters. This means that every snirf file loaded will have the same parameters applied to them. If you think a parameter should be on a per file basis (such as Age, Gender, Group) and not on a global basis, raise a [feature request](https://git.research.dezeeuw.ca/tyler/flares/issues/new) along with an explanation as to why you think it should be on a per file basis. -Good to know information before reading this Wiki page includes a brief understanding of data types to ensure that the correct values are inserted. Here is a short explaination of data types that FLARES uses: +Good to know information before reading this Wiki page includes a brief understanding of data types to ensure that the correct values are inserted. Here is a short explanation of data types that FLARES uses: - bool - A boolean data type. This includes True or False, but can be represented by a 1 (True) or a 0 (False). - int - An integer data type. This includes whole numbers without fractions or decimals (-23, 5, 0, 10). - float - A floating point data type. This includes numbers that contain fractions or decimals (-23.0, 4.12, 22.8) - list - A list data type. For FLARES, all lists will be available in a dropdown. It is only required that one item in the list be selected. - range - A range data type. For FLARES, all ranges will be present as an int, -- str - A string data type. This includes any character or gouping of characters (hello, 5t6y7, this is a string!). +- str - A string data type. This includes any character or grouping of characters (hello, 5t6y7, this is a string!). Any parameter that has been changed from its default value will appear with blue text and bolded, and any parameter that is advanced will have the `⚠️` symbol next to it. @@ -155,7 +155,7 @@ Determines what to do with channels that were marked as bad in the previous qual - BAD_CHANNELS_HANDLING (list, default=Interpolate): How the bad channels should be dealt with. - ⚠️MAX_DIST (float, default=0.03): Maximum distance to look for potential neighbours to interpolate from in meters. - ⚠️MIN_NEIGHBOURS (int, default=2): Minimum number of neighbours inside the distance threshold required to interpolate from. -- MAX_BAD_CHANNLES (int, default=12): Maximum number of bad channels a participant can have before they are eliminated. This considers hbO and hbR as separate channels, and this value is exclusive. +- MAX_BAD_CHANNLES (int, default=12): Maximum number of bad channels a participant can have before they are eliminated. This considers HbO and HbR as separate channels, and this value is exclusive. Note: If BAD_CHANNELS_HANDLING is not set to `Interpolate`, ⚠️MAX_DIST and ⚠️MIN_NEIGHBOURS will be ignored. Note: If BAD_CHANNELS_HANDLING is not set to `Remove`, MAX_BAD_CHANNELS will be ignored. @@ -181,7 +181,7 @@ TBD. Note: If WAVELET is set to False, IQR, WAVELET_TYPE, & WAVELET_LEVEL will be ignored. ## Haemoglobin Concentration -Calculates the haemoglobin concentration of the data. This process is documented better at [this link](https://mne.tools/stable/generated/mne.preprocessing.nirs.beer_lambert_law.html). This process is a required step, with all parameters being advanced so the header will only appear if `Show Advanced Parameters` is selected. +Calculates the haemoglobin concentration of the data. This process is documented better at [this link](https://mne.tools/stable/generated/mne.preprocessing.nirs.beer_lambert_law.html). This process is a required step, with all parameters being advanced so the header will only appear if `Show Advanced Parameters` is selected. **Parameters:** - ⚠️OVERRIDE_PPF (bool, default=False): TBD. @@ -293,7 +293,7 @@ This stage just involves some under-the-hood calculations that will be used for Section containing other variables that can be important but do not affect the analysis in any shape or form. **Parameters:** -- MAX_WORKERS (int, default=6): How many .snirf files can be processed simultaneously. More powerful devices can specify a higher value, but must have both the CPU and RAM available. It is estimated that an individual participant will require a peak of around 2GB of RAM. Will allow for the value of 'auto' in the future. +- MAX_WORKERS (int, default=6): How many snirf files can be processed simultaneously. More powerful devices can specify a higher value, but must have both the CPU and RAM available. It is estimated that an individual participant will require a peak of around ~2GB of RAM. This will allow for the value of 'auto' in the future if you are unsure what your setup supports. - ⚠️VERBOSITY (bool, default=False): True if the log file should contain more details, False if the log file should only contain minimal details. Should be set to True when raising an issue with the application to provide helpful information to the developer. # What's Next