Notes:

Release Name: v2.2

Notes:
The release has been verified in Matlab 2016a.

The homer2 scripts in the zip file run in matlab on windows, mac, and linux. Documentation on how to run these scripts can be found at http://homer-fnirs.org .

The Homer2_UI and AtlasViewerGUI stand alone executables are now installation packages for Windows and MAC. Running the setup.bat (or setup.command for MAC) will install both executables.

See README.txt in the installation packages for more details about the installation process.

The packages were built using 64-bit Matlab R2016a . To run the executables, you need to download and install the R2016a 64-bit MCRInstaller that is freely provided at the mathworks website
http://www.mathworks.com/products/compil...

Changes:
Homer2_UI:
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Change HbX line style in data axes display so that HbO, HbR, HbT are constant line styles. HbO is solid. HbR is dashed. HbT is dotted

Changed channel colors of the first few time course data from red, blue and green to orange, green and magenta to avoid confusion with oxy and deoxy HB.

Fixed bug where time course colors for multiple channels in the data display don't match the channel colors in the SDG axes display.

Added function and menu option to a) downsample a nirs file and b) create a new nirs file from existing one which only has a specified segment of the original data.

Alert user if there's error when calculating HRF by displaying message box with the error and name of function which failed.

Fix bug when loading and fixing SD.SpatialUnits, bad channel info in SD.MeasListAct of the 2nd ... Nth .nirs file is overwritten by the first .nirs file's SD.MeasListAct. Katherine Perdue submitted this issue.

Processing Options GUI window being too long and going beyond screen boundaries in a small screen.

Fixed issue when starting Homer2_UI and an error is encountered in loaded .nirs files, the error message box display goes off screen on small laptop screens.

Made procStreamGUI.fig resizaeble, and increased font size becasuse really hard to read on smaller screens.

Fix for db2.mat file not found in Homer2_UI.exe when performaing motion correction with hmrMotionCorrectWavelet.m. This is only a problem in the standalone executable and on Linux.

Added wavelet motion correction function hmrMotionCorrectKurtosisWavelet.m and supporting function written by Antonio Maria Chiarelli.

Enabled stimGUI and procStreamGUI resizing.


AtlasViewerGUI:
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Updated iso2mesh with the latest code from http://iso2mesh.sourceforge.net/cgi-bin/... Iso2mesh is used in AtlasViewer to convert Freesurfer processed MRI files to AtlasViewer format. Previously it only worked on Windows. The update and fixes makes it work on MAC and Linux.

Fix error generating Monte Carlio output when the file path to the input, output or Monte Carlo excutable has spaces in it as can happen on Windows.

For Matlab versions 2014b, 2015a, and 2015b, display warning when using Find Refpts menu option. This option lets the user pick the Cz, Iz, LPA, RPA, and Cz head reference points from which 10-20 points can be calculated. The warning states that there is a bug in Matlab versaions 2014b, 2015a, and 2015b in the graghics which causes the datacursor to attach to vertices on the the hidden side of the head instead of the selected vertex on the visible side. This issue was fixed in R2016a (9.0). Also this issue doesn''t exist in versions prior to R2014b (8.4), for example R2013b.

If digitized points files are detected in subject's sub folders (rather then it's own subject folder) then give user a choice to load them or not. This is relevant to group imaging with several subjects all with the same probe digitized.

When overlaying HbConc group average, import probe that is the mean of digitized points of the group subjects instead of design probe.
Increased the size of the ref point markers on the head in Find Ref Points.

Fix loading of fluence files errors after saving atlas viewer state of registered probe then restarting atlasviewer and reloading fluence files got error that voxPerVoxel field nonexistent.

Fixed iso2mesh used to resample meshes in Freesurfer-to-Viewer conversions

Fixed saveRefpts not saving correctly when using Find Ref Pts feature and changed functionality to allow overwriting atlas ref pts and displaying a warning. By contrast overwriting ref pts in local subject dir doesn't produce warning, only a message informing user that old refpts will be moved to refpts*.old. The bug was due to an incorrect path in refpts telling you where the ref pts came from.

Fix bug in probe placement variation to account for the fact that short separation detectors are thrown away.

Added ability to AtlasViewerGUI to overlay image of Hb Concentration on the cortex, using the .nirs files HRF data produced by Homer2.

Changed menu options in AtlasViewerGUI, related to probe projection by consolidating channels and optodes projection to one menu option, 'Project Probe to Cortex'. The user then chooses if they want to project optodes or channels.

Add lower resolution one wavelength fluenceProf files to homer2.

Fix in AtlasViewerGUI to Freesurfer-to-Viewer conversion.

Display waitbar when saving viewer state because it takes about 10-20 seconds, to let the user know what's going on.

Added code to AtlasViewerGUI to display the saved state of the Hb Image Reconstruction. It was being saved but not displayed when the GUI starts up.

Added checkbox to probe placement displays to toggle between AtlasViewer and MNI coordinates.

Changed the color of the head and pial surfaces to be more pleasing to the eye.

Reduced the shininess of the light on surfaces.

Changed the lighting to be spread evenly over the surfaces.

Fixed left-right side flipping problem in probe placement variation feature in AtlasViewerGUI.

Fix bug in orientation when converting Freesurfer files to AtlasViewer.

Fix for matlab error when loading nirs files without tHRF.

Added user configuration of max/min tHRF range in HB Concentration overlay calculation.

Fix matlab error in AtlasViewerGUI, when dummy optodes don't exist.

Fix error in AtlasViewerGUI, Hb Image reconstruction, where HbO is always displayed when changing channels, even when HbR is selected.

Added ability to select channel in Hb Concentration display.

Changed color of cortex in Image Display objects.

Greatly simplified image display panel in AtlasViewerGUI where sensititivity and image reconstruction are displayed.

When importing probe, If probe is misaligned warn user about it and ask if they still want to try to project (register) probe to head.


SDgui:
--------

Fix problem of inability to select optodes with the mouse in some instances like with a dense probe.

Fix bug where user starts SDgui, cancels .SD file search in order to create new probe geometry, then enters coordinates of first optode which generates matlab error.
When saving file in SDgui, made .SD extension the default extension when user doesn't provide an extension.


Miscellanious:
----------------

This release's homer2_install*.zip installation package was built with Matlab R2016a (instead of R2014b used in previous release). Users of the stand alone executables have to download and install Matlab Compiler Runtime 2016a.

Created function checkToolboxes.m, and checkToolboxes_Homer2.m and checkToolboxes_AtlasViewer.m to check if the required toolboxes for these tools are installed and if not to warn the user about it, listing which toolboxes are missing. Added this check to setpaths and also added list of required toolboxes to README.txt.

Update setpath to check matlab compatibility if required toolboxes exist.

Added setpaths.m for setting the Homer2 and AtlasViewer search paths in matlab, every time a new matlab session is started.

Added ability to remove the homer2 paths using the command setpath(0).

Created homer_install installation packages for Windows, MAC and Linux for installing and running Homer2 and AtlasViewer standalone executables.