Release Name: v2.2
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
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
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
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
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.
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
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
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
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
Fix for matlab error when loading nirs files without tHRF.
Added user configuration of max/min tHRF range in HB Concentration
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.
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.
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
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
Created homer_install installation packages for Windows, MAC and
Linux for installing and running Homer2 and AtlasViewer standalone