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[Sticky] NEW RELEASE: Homer3 v1.31.2


Stephen Tucker
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Hi Homer3 community!

A new version of Homer3 has been compiled for release. The MATLAB Runtime executable and source code is available here!

This version has a whole bunch of new features and fixes. Some major features include...

-- Processing stream user parameters can now be arbitrary length. That means user has to know how many elements to enter for specific cases. For example for hmrR_OD2Conc which converts optical density (OD) to concentration (conc), the user parameter associated with it is partial path length (ppf). It is no longer fixed length at 2 as was previously but instead is equal in length to the number of wavelengths associated with OD.

-- The processing stream is now checked for errors in the order of the functions. This is done when the user constructs the processing stream in ProcStreamEditGUI or when running it in MainGUI. Meaning that if the order of the functions does not make sesnse the processing stream will not be run and instead an error will be displayed.

-- Incorporated mlActMan and Auto to tCCAGLM functioNow the function gets only the active long and short channels (that is determined by mlAct Mand and Auto) in tCCA filter calculation and regressor generation. Also changed ss_ch_inx to ss_ch_on, now user will choose whether ss channels should be included in tcca or not (not a list of channels). Possible future issue: if different channels are active for the rest versus experimental run.

-- Added application settings GUI, which dynamically loads all the parameters in the Homer3 configuration file (AppSettings.cfg) and allows user to change the value of those config parameters. It can be launched either on its own or from Homer3 ile menu.

-- Fully implement SNIRF stim amplitude data column. Before the amplitude column was used as a way to set the active/inactive state of a stimulus. Also implement change in the SNIRF spec where an arbitrary number of columns are allowed greater or equal to 3. Lastly implement the SNIRF stim naming of columns with the stim dataLabels field.

-- Add new user functions hmrR_PreprocessIntensity_MedianFilter, hmrR_PreprocessIntensity_NAN, hmrR_PreprocessIntensity_Negative to prevent bad data values from disrupting your processing

-- Add new user function hmrR_PreprocessOD_LinearFit to perform a linear fit and remove it from the time course data.

-- hmrS_runAvgStd change: hmrS_runAvgStd is modified. Now it gets a weighted average of single run stds. Old version is archived.

-- Added Zoom and Pan functionality to probe display in main GUI to allow zooming in and out of different parts of the probe.

-- Fix reporting of date and time in Homer3 output. This caused a matlab error in time zones with a different date string format.

-- Child GUIs like PlotProbe and StimEditGUI do not synchronize browsing through the data files with the MainGUI, at least not by default. That is when selecting files or folders in MainGUI the data in the active child GUIs does not not change to match the currebtly selected file/folder in MainGUI. That can be changed by clicking on the Tools --> Synchronize Browsing menu of the child GUI

-- Automatically excluded/pruned channels are now displayed in the probe plot as in Homer2

-- hmrR_GLM now outputs t-statistics for the beta weights estimated by GLM, and the p values corresponding to the t-statistics obtained. By default, GLM outputs output.misc.hmrstats that has the t statistics results for the hypothesis of whether any of the beta weights are statistically different than zero. Given a contrast vector is provided by the user, GLM now also outputs t-statistics results for the hypothesis of whether the beta weights for any given condition(s) is statistically different than the beta weights for another condition(s). 

Please let us know how you find the release, and if you run into any issues using it. As always, we welcome any feedback/suggestions, and thank you for your help in developing Homer!

 

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