Release Notes v2.8
-- Fixed time course not filling up entire length of x-axis. Made a
mistake last time I did this because I broke setting fixed x-range.
This time I am putting the setting in the auto xlim section.
-- Another fix to EasyNIRS_ProcessOpt.m when there are too many
functions in the proc stream EasyNIRS_ProcessOpt GUI cuts off
-- Another fix to checkNIRSFormat when .nirs files missing t,d,or
SD they should not be considered valid data files and should be
-- Added on/off switch for enabling/disabling the following user
function in a processing stream :
-- Added fixed time ranges options for X and Y axes in HOMER2 GUI.
-- Homer2_UI GUI and procStreamGUI both go off screen at the bottom
and are too big for some screens. Made units normalized and so that
size is relative to screen size and location to fit completely on
-- Added function resetGroupFolder.m (can only be used if running
Homer2_UI from Matlab) to reset subject folder nirs files back to
-- Modified hmrFlowInput.m
-- Got rid of popup warning that db2.mat doesn't exist. Instead
just print in Command window and save generated db2.mat, without
prompting user to click OK button.
-- Changed the default iqr to 1.5 in hmrMotionCorrectWavelet.m.
-- Change plot line styles for HbR and HbT displays to be dashed
(--) and dotted (.-) lines respectively to distinguish from HbO
displays. Same for wavelengths 2nd (or 3rd) wavelengths when
viewing raw data or OD.
-- Correct for nan values in intensity(n) in hmrFlowInput.m
-- Added of Standard Views which has buttons to view any head
anatomy Left/Right, Anterior/Posterior, and Superior/Inferior
sides. You can also use two angles, azimuth + elevation to specify
precise views of any head.
-- Added tool ImportMriAnatomy to be able to import into
AtlasViewer any subject-specific MRI anatomy in NIFTI and MGH
-- Change what is displayed at startup when digitized points are
present in the subject folder: previously only thew digitized
points were displayed. Now all the anatomical pieces that are
available in the subject folder - head, brain, etc - are displayed.
-- Added menu option Reset Viewer State to be able to start
workflow from scratch.
-- Added support for loading high-resolution fluence files.
-- Improved EEG reference points calculation tool:
a) Consolidated reference points menu items Find, Show, Configure,
Calculate under one menu item: "Reference Points" under Tools menu.
b) Calculate ALL 10-5 eeg reference points to allow selection of
10-20, 10-10 or 10-5 without having to recalculate them every time
you select them. Improve progress bar display when calculating eeg
points to meaningfully show progress in one bar.
c) Recalculated default 10-5 reference points for Colin atlas based
on new definition of the ear landmarks, using the preauricular
points LPA and RPA, rather than tragus which is what the previous
ref points were based on.
d) But added a configuration tool menu item, allowing user to
specify the anatomical location of RPA and LPA before recalculating
10-20, 10-10, 10-5. This is to allow for some ambiguity in the
standard definition of the ear points in the literature.
-- Improvements to Find Ref Points tool:
a) Show in the selection buttons which reference points have been
selected and which haven't;
b) Datacursor position display is now in a separate window to the
c) The Save and Rotate Zoom panel is now in a separate panel.
d) Centered head display so it's not so close to the panels and
isn't obscured by the panels.
e) Fix issue which causes the display to suddenly zoom make the
head become huge when user clicks the figure's pan button (i.e.,
the small button in the figure toolbar with the up-pointing hand
f) Fixed bug in the Find Ref Points GUI where re-selecting a
reference point position, instead of repositioning the reference
point under and keeping the same label, it would assign it a
g) Handle situation when user selects a ref point with one of the
ref points buttons but has not selected head location with the data
h) Removed TIP about orientation from Find Ref Points tool which
forces user to read a lot of text, and stop to click OK and is
non-visual. Instead added labeling of sides as L and R according
which side of the head is the actual left and right.
-- Fix matlab error when trying to plot image recon without first
-- Fix when starting AV from a saved state (ie. when
atlasViewer.mat is present in the subj folder), incorrectly setting
Forward Model menu options. Even though probe is registered to
head, and Adot sensitivity is available we don't enable all the
downstream options like Load/Generate sensitivity.
-- In ImageRecon GUI get the appropriate subject name rather than
naming everything 'New Folder'
-- Should not be generating additional simulated wavelengths for
DRM protected fluence files in setpaths - atleast not by
overwriting the files.
-- Fix typo in bug fix when updating the number of wavelengths
fwmodel.nWavelength when loading fluence profiles. Xinge uncovered
-- Added feature to allow other atlases to be installed by user as
the set of atlases offered by AtlasViewer when using Change Atlas
-- Eliminated the need for user to have to find and rename
atlasViewer_SDdesign.mat in Probe Placement Variation.
-- Fixed bugs related to loading groupResults (generated by
Homer2_IU) in AtlasViewerGUI for image reconstruction and HbConc.
-- A Homer-users list member posted that he could not get AV to
generate sensitivity matrix by following the YouTube video that
shows how to do this. The reason for the problem of not being able
to generate sensitivity was that the digitized probe in the
digpts.txt file didn't match the probe in any of the .nirs file in
his subject folder and therefore the measurement list could not be
imported. To generate the sensitivity profile AV has to import the
measurement list from one of the .nirs files in the subject folder.
It will not do it if it detects an incompatibility. Added warnings
and error messages alerting user when the measurement list is
missing and therefore the ensitivity profile cannot be generated.
-- Fix for probe with 'cm' units appearing incorrect because
AtlasViewer was not using the Spatial Unit parameter in the SD
-- Fix for matlab error when clicking the Image Recon button in the
ImageRecon GUI because Matlasb's eigs function in
hmrImageReconConc.m doesn't work for single-precision floats only
double. The sensitivity profile in some cases is single precision.
-- Regenerated fluence profile with 1e7 instead of 1e6 photons.
-- Change when some Forward Model menu options are enabled based on
availability of Monte Carlo output and sensitivity profile.
-- Fix artifacts appearing in head surface because when generating
surface from head we were keeping segmentation layers instead of
making the whole head one value which would have been the correct
-- Fix matlab error when retrieving digitized points because
isalpha_num is undefined in matlab versions later than R2016a.
-- Allow probe registration and other functions (for example when
clicking pushbutton Register Probe To Surface) even when ONLY the
head surface but not the head volume or brain surface are part of
the AtlasViewer imported anatomy. Previously AtlasViewer expected
head volume, brain surface and head surface to be present for it to
be able to do anything like probe registration.
-- Improve noise reduction code for head volume when importing
subject-specific anatomy. Old method didn't work well esp. for SPM
output. Added adaptive thresholding where AtlasViewer tries to
figure out automatically the threshold below which pixel values are
considered noisy in an MRI image.
-- Fix Register-to-Head-Size menu tool matlab error.
-- Added feature to calculate and display head dimensions;
circumference, and length of sagittal and coronal curves.
-- Search for anchor points in reference point labels using
incomplete string comparison when registering spring probe. It
incorrectly assumed reference point labels are always lowercase.
-- Fix matlab error when registering SD probe with springs after
having registered the atlas to dig points. Found by Xinge who tried
to compare designed flat probe with the digitized probe.
-- Check the consistency of the main pieces of the loaded anatomy;
make sure they all come from one source and is not a patchwork from
atlas and subject folders.
-- Added ability to build Monte Carlo executable on-the-fly if it
-- Fix AtlasViewer not recognizing that an Monte Carlo executable
has been found and still asks user to locate it. Happens when the
MC executable has been been built on-the-fly when starting
AtlasViewer. Encountered this bug on Linux.
-- Fix executable permissions problem when running Monte Carlo on a
-- Fix for Matlab error when importing subject specific anatomy on
dyld: library not loaded /opt/local/lib/libstdc++.6.dylib
Not all MACS produce this error. It happens when resampling the
volume (using meshresample).
-- Added popup message asking user wants to select reference points
and calculate EEG points at the end of importing MRI anatomy.
-- Fix for bug seen in fNIRS course 2017 in image reconstruction
which complains that 2 wavelengths are needed, because the
precalculated fluence files with one wavelengths were loaded. This
bug only occurred in the homer2 source release but not in the exe
installations. Fix is to simply enable simulating a second
wavelength in setpaths.m.
-- Fixed View Origin feature which wasn't working. It was giving a
Matlab error instead.
-- Fix bug where after 1) registering atlas to dig points, 2)
clicking "Register Probe to Surface", 3) running Monte Carlo 4)
generating sensitivity, then 5) restarting AtlasViwer, and then
repeating steps 1) and 2) AtlasViewer gets stuck trying to register
probe to surface. (This is because the center of the transformed
volume was not calculated correctly.)
-- Fixed Matlab error when loading group mean digitized points.
-- Fixed small bug in zoom where every time you restart AtlasViewer
or find new ref pts it zooms in closer in the main GUI.
-- Fix initial zoom of head surface when redisplaying axes (for
instance after selecting basic reference points and calculating
10-20 reference points.)
-- Added the probe editing tool developed by Ardalan Aarabi -
Université de Picardie Jules Verne. The tool allows changing the
location of an existing optode on head (either digitized or
-- Added ability to delete multiple optodes and associated channels
by dragging mouse over optodes in the SD axes display. Previously
you could only delete optodes one at a time and only from the table
of optode positions.
-- Added checkbox to view full path of the loaded SD file.
-- Made GUI fonts for MAC and Linux bigger. Matlab fonts are
smaller on MAC and Linux than Windows.
-- Clean up of SDgui:
* Resize and reposition GUI.
* Make all table labels more visible.
* Show axes X and Y axis labels more clearly using the latest
matlab version method.
* Reposition text box for error messages and file load/save
messages to make them more visible.
-- Fix matlab error when saving SD file with number of springs is
shorter than 3.
-- Changes to setpaths to remove any paths from other Homer2
workspaces that conflict with the currently active Homer2. This
change not relevant to Homer executables, only when running from
-- Fix broken installation process for MAC
-- Fixed sizing and positioning issues for Homer2_UI and
AtlasViewerGUI GUIs so that it looks reasonable on any screen or