BrainWave ARCHIVE

BrainWave version 2.2 software.
BrainWave version 2.2 documentation

New Features:
- An improved and much less "beta" version of the MRI Viewer module which allows importing raw MRI data, setting fiducial locations, segmentation and viewing of MRI surfaces (using SPM or FSL) and creation of head models, etc.
- Ability to use a “surrogate” MRI lieu of a subject's actual MRI scan (e.g., a template brain) for group averaging by warping the image to the subject's head shape, and the ability to specify different templates for spatial normalization of group images.
- Ability to epoch and analyse Elekta/Neuromag continuous data files (using the Neuromag fiff2ctf conversion).
- Ability to view individual subject, and group waveforms and time-frequency plots in the same plot window, as well as change bandpass and baseline, scaling etc.

BrainWave version 2.4 software.
BrainWave version 2.4 documentation

Minor bugs fixes:
- pseudo-F option was not executing - fixed
- reading of saved settings file has been fixed
- BW will allow you to locate FSL directory if the FSL_DIR environment variable not defined
- will now read single and multi sphere head model (.hdm) files created with CTF software
- a Matlab GUI issue was causing a .rpt extension to be inserted into file names
- mex functions were not running on some older releases of Linux, have been recompiled with gcc 4.1

Some new features in this version:
- Data Import - can now load latencies from multiple input files (append instead of replace)
- MRIViewer program will now allow you to save and reload and view head models from .hdm files
- MRIViewer will now save in the CTF MRI (version 2) MRI format.
- Average / Permute Images - will automatically compute both positive and negative contrasts.
- Average / Permute Images - will allow averaging of .svl images (e.g., for averaging multiple images from same subject).

Important notes:
-32-bit versions of Windows and Linux will no longer be supported.

BrainWave version 3.0 BETA software.
BrainWave version 3.0 BETA documentation

New Features:
- Compute cortical surface based 4D beamformer images with orientation constraints (compatible with CIVET or FreeSurfer surface meshes).
- New viewer for surface based images with coordinates mapped to MEG and MNI/Talairach coordinates.
- Improved interface for group images with the option to generate contrast images.
- Data import now allows for downsampling, latency correction, automatic trial rejection and sensor re-alignment due to head motion (CTF CHL required)
- Optimized file organization for improved file re-loading capabilities.
- Utilize multiple datasets for the calculation of covariance matrices or baseline windows.
- Have the MATLAB Signal Processing Toolbox? Use Hilbert Transform to compute power envelope for virtual sensors, time-frequency plots.
- ...and much more!

BrainWave version 3.1 software.
BrainWave version 3.0 BETA documentation *unchanged text

New Features:
- In addition, we have made multiple minor aesthetic changes for better cross-platform synchrony (Tested on versions Windows 8.1, Linux Fedora 18 and Mac OS X 10.10).
- No brain surface data? Now you can display SPM normalized images on a default a Freesurfer-based CH2 (adult) template surface for a 3D preview (including inflated brain).
- Plot VS button added to Single Subject Analysis to allow user to create VS/TFR plots when a peak location is already known.
- Add/Delete Condition files option added to Group Analysis window.
- Added Shaded standard error option in group time course plots.
- Single Subject VS plots now able to display single trials (overlaid).
- New option to plot RMS over a time window on the topoplot in Plot Data window.
- Defaults changed:
1) Default number of TFR cycles to 7 from 5
2) Default covariance regularization (10 fT per root Hz RMS) is now enabled by default (Data Parameters window)

Bug Fixes (3.0 beta):
The following bugs were identified and corrected in version 3.1:
- Downsampling was shifting epoch event placements.
- SPM occasionally cutting off frontal lobe during normalization. Default bounding box is now slightly larger in x and y directions to accommodate larger heads or rotated fiducials.
- Group analysis error setting default params
- Excluded trials were not being recognized in Import Data
- Group analysis “Use Condition 2 as SAM Baseline” option was being ignored.
- MRIViewer could not import some Philips MRI DICOM files. Fixed by have option now to use dicm2nii OR SPM to import DICOM files.
- Left and Right ear fiducial labels were mislabeled (swapped).
- Thresholding was not working on inflated cortical surfaces.
- CombineDs was not updating head coil positions.
- Changing the search radius was not updating.
- Bitmap (.bmp) images were not being saved.


**NOTE: Due to some default changes in MATLAB 2014 (and newer), some aspects of the graphics interface (e.g., font size) may appear different or may lead to odd errors. We are working to upgrade these changes.
**SUGGESTIONS: Try increasing your screen resolution or try an earlier version of MATLAB (2013b tested). If you continue to experience display issues, please email us.

BrainWave version 3.2 software.
BrainWave version 3.2 documentation

What's New:
Import MEG Data:
- Improved layout
- Ability to load and epoch multiple input datasets at once, with auto-naming using default fields for subject name, condition, and marker
- Alternative batch mode for epoching multiple datasets

MRI Viewer:
- Heat Maps! Color overlays of beamformer images on subject's MRI (load .svl from menu or launch directly from 3D glass brain view). View max peak location and adjust thresholds.
- Improved menus and new buttons to navigate to overlay peaks / dipoles

Group Image Analysis:
- Improved interface and study management
- Load a previous study directly from the main menu
- Easy selection of different methods for computing beamformer weights, including combined (common) weights for two-condition contrasts, or select custom covariance data.
- Previously computed imagesets for each study can be quickly re-plotted from pulldown menu

Group VS Analysis:
- Generate contrasted (difference( waveforms between two groups.
- Generate VS plots from multiple conditions in same dialog.
- Aternate covariance (weight) datasets are automatically saved and reloaded from imagesets

3D Surface Rendered Images:
- An auto peak finder generates a list of peaks within a specified radius.
- Generate permutations directly from group peaks selected.

General:
- added compatibility with SPM12
- multiple bug fixes and internal streamlining of code for better stability
- Improved tutorials and documentation - now easier to read step-by-step instructions.
- NEW File type: Old .vlist files have been replaced with new “virtual sensor” (.vs) files which specifies both dataset to use for VS calculation and the “covariance” dataset for weight calculation.


**NOTE: Due to some default changes in MATLAB 2014 (and newer), some aspects of the graphics interface (e.g., font size) may appear different or may lead to odd errors. We are working to upgrade these changes.
**SUGGESTIONS: Try increasing your screen resolution or try an earlier version of MATLAB (2013b tested). If you continue to experience display issues, please email us.

BrainWave version 3.3 software.
BrainWave version 3.3 documentation

BrainWave version 3.3 BETA software.
BrainWave version 3.3 BETA documentation

What's New (version 3.3 BETA):
- FIFF2CTF - Elekta/Neuromag users are now able to convert raw fiff data into CTF on Linux OS (Mac OS version pending) with an integrated marker extraction tool.
- Enhanced data importing routines for Yokogawa-KIT data.
- Users now have the option to use SPM8 or SPM12
- Overlay calculated SAM images (heat maps) onto subject MRI.
- Windows 10 and Mac OS X Sierra tested
- Improved features in each module, e.g., auto-naming imported datasets
- Improved module window positioning (a special need for Windows users)
- ...among other great, easy-to-use features

Changes / bug fixes for version 3.4 (Jan 2018)
1. MRIViewer
- MRIViewer.m will now automatically delete (with warning) existing SPM warping files (all _reslice_ **) that exist when you save the fiducials (.mat). This will eliminate the need to manually delete such files when re-saving fiducial positions.
- change subroutines (bw_generateFSLMeshFiles.m and bw_FSLmesh2shape.m) so that will run FSL up to version 5.0.10 i.e., will automatically look for both .vtk or .off files.
2. Import Data
- fixed bug (bw_import_data.m) where correct marker data was not being read when multiselecting datasets and then using batch mode.
3. combineDs
-fixed bug in C++ code (bw_combineDs.cc) that was corrupting the sensor positions for the combined datasets.
4.Group Image module - new features
- when combining datasets, BrainWave now copies head model files from the first condition to the combined condition so that it can be used for image creation. This will eliminate the need to manually copy head model files for new combined datasets.
- added a "Combine Conditions" menu item in the File Menu that provides easy way of combining already epoched conditions into a single condition. Naming convention is slightly different (doesn't repeat the subject ID) so won't overwrite the ones created by combineDs. Changes to bw_group_images.m and bw_getConditionList.m
- Added a "Copy Head Models" menu item to the File menu. This provides convenient way of copying the head models from one condition to e.g., a condition of newly epoched dataset without having to do this through MRIViewer (or manually...). Changes to bw_group_images.m.
5. Minor Bug Fixes
- Add movegui to bw_group_images.m for Add Conditions to bring entire window to mid screen. Previously windows are offscreen for some computer resolutions.
- Add movegui to bw_eventMarker.m to bring entire window to mid screen. Previously offscreen for some computer resolutions.

**NOTE: MATHWORKS is aware of graphics incompatibilities for some 2015-2016 versions of MATLAB which has a notable effect on some applications of BrainWave. Thus, it is highly recommended to use MATLAB 8.3 (2014a) or earlier for Mac OS users. Later versions (e.g., Sierra) may require additional patches to run MATLAB graphics until the proposed MATLAB 2016b release found here and here. The installation of legacy Java may also be required (see here)
**SUGGESTIONS: Try increasing your screen resolution or try an earlier version of MATLAB (2013b tested). If you continue to experience display issues, please email us.