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| ==== Source modeling ==== * Implementation of a new unified minimum norm/beamformer framework (work in progress) |
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| * Merging the 12+3 introduction tutorials to illustrate better the latest developments ==== Source modeling ==== * Implementation of a new unified minimum norm/beamformer framework |
* Standard workflows for different types of data and experiments (work in progress) * Cross-validation with MNE and FieldTrip: <<BR>>http://martinos.org/mne/dev/auto_tutorials/plot_brainstorm_auditory.html |
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| * Significance thresholding of the connectivity matrices | * Significance thresholding of the connectivity matrices (not started) |
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| * Removing the dependence to the Java interface to run in headless mode * Interacting directly with distributed computing systems ==== Compatibility ==== * Reading and writing FieldTrip structures * Calling FieldTrip functions from the pipeline |
* Removing the dependence to the Java interface to run in headless mode (not started) |
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| * Nicer 2D topographies, standardized (using FieldTrip .lay files?) | * 2D topographies: * Nicer topographies with circle around 2DDisc (similar to EEGLAB plots) * Standardized plots (using FieldTrip .lay files?) * Aligned on the midline at least * Contour lines sometimes messed up with Elekta recordings * Make the surface on which the values are interpolated simpler * MEG/EEG registration: Apply the same transformation to multiple runs * Montages: * Separators (" : MLC11" already works, could be just " : "), should add an empty space. |
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| * Same shortcuts as the raw file viewer (right-click + move for gain) * Add support for montages |
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| * Show easily the maximum value at the current time point | |
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| * Events: Change the category of a selected event easily, instead of deleting/marking new | |
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| * EEG reference/storage: * Bad channels specified at the program level (for sites that have permanent bad channels: AS) * NIRS: * Add new data type * Display of sensors by pairs oxy/deoxy (red/blue) * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] * Can be done with Matrix > View as image: extract cluster, concatenate for all trials * Filtering: * Use short FIR filters instead of IIR for bandpass, to limit the ringing * Or allow the users to edit the LowStop parameter in bst_bandpass. * Show easily recordings maximum/values in the file viewer |
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| * Start Brainstorm without Java (-nodesktop) * Allow FieldTrip functions in compiled version * Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly |
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| * Manage multiple custom colormaps | |
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| * Open new windows as tab | * Open new figures as tab (docked in the Figures window) |
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| * Display warning before opening files that are too big * Smooth display from figure_image (ERPimage, raster plot...) |
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| * t-tests on connectivity measures | * Stat tests on connectivity measures * Connectivity on unconstrained sources: how to group the three orientations? * Review by Jan-Mathijs: http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full * Connectivity based on band limited power (Sylvain): * Compute Hilbert/Bandpass + correlation of the envelopes * Bandpass envelopes before computing correlations? * Compute Hilbert(sensors) and then project to source space? |
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| * Does not work on Matlab 2015a | * Does not display negative values correctly (correlation or difference of coherence) * Re-write using pure Matlab code and smoothed graphics |
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| * Fix zoom in one region | |
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| * Re-write using pure Matlab code and smoothed graphics | |
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| * NxN on sensors: does not place the sensors correctly in space | |
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| * Average cross-spectrum instead of concatenating epochs (to avoid discontinuities) | * Average cross-spectra instead of concatenating epochs (to avoid discontinuities) |
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| * Add progress bar management | * Add progress bar |
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| * Add input TF , to disconnect TF decomposition and PAC computation (Peter) | |
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| * PAC maps: Display all sensors at once (like TF and DynamicPAC) * Time-resolved correlation/coherence: Display as time bands |
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| * Multi-tapers? | |
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| * Connect NxN: Display as time series > Display warning before trying to open too many signals | |
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| * PLS: * https://www.rotman-baycrest.on.ca/index.php?section=84 * meg-pls dot weebly dot com * Krishnan 2011: http://www.ncbi.nlm.nih.gov/pubmed/20656037 * Cheung 2015: http://www.sciencedirect.com/science/article/pii/S1053811915007648 * McIntosh 2012: http://www.ncbi.nlm.nih.gov/pubmed/22804773 * McIntosh 2004: http://www.ncbi.nlm.nih.gov/pubmed/15501095 * Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow |
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| * Export IC time series (and then compute their spectrum): solves the problem above | |
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| * Distributed processing: Brainstorm that can run without Java | * Display of spectrum for components (PSD/FFT) * Use FastICA (algo crashing) * Understand why EEG/Epilepsy tutorial data crashes if we don't limit the number of components * Add components preselection: Correlation with EOG/ECG * Import ICA matrices available in EEGLAB .set files * EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm<<BR>>(http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA) |
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| * Call FieldTrip functions from pipeline editor * Optimize opening time for the menu "Add process" * SSP:<<BR>> |
* SSP: |
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| * Rewrite without the force low-pass filter at Fs/3 | * Rewrite without the forced low-pass filter at Fs/3 |
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| * Rewrite to have the same input as coherence * Normalize with the total power (TF/sum(TF,3)) |
* Rewrite to have the same input as coherence (frequency resolution instead of window length) * Use the progress bar |
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| * Interpolate the bad channels | |
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| * Do not display the intermediate files | |
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| * Standardize using: diff before calculation + cumsum (checkbox "flatten data") * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...) * Display logs as negative |
* Multi-tapers * Short-time Fourier transform: http://www.mikexcohen.com/lectures.html * Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc * Bug: Display logs as negative * Bug: 3D figures: Colormaps with "log" option doesn't work * Bug: Difference of power displayed in log: problems (Soheila) |
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| * Impossible to keep complex values for unconstrained sources * Pad short epochs with zero values for getting lower frequencies * Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead. * Extend clusters tab to display of TF to overlay TF signals (Svet) * When normalizing with baseline: Propagate with the edge effects marked in TFmask |
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| * Detection of bad segments in the RAW files (Beth) | |
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| * Allow the detection on differences of signals (bipolar montages) * Average: * Remember how many trials were used per channel * Save standard deviation * Display standard deviation as a halo around the time series |
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| * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html * Other processes:<<BR>> |
* Other processes: |
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| * Use field process field "Group" to separate Input/Processing/Output options * Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd |
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| * Optimize startup speed * Start Brainstorm without Java (-nodesktop) |
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| * Group matrix files => allow to process matrix files by trial types | * Matrix files: Allow to be dependent from other files |
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| * Allow matrix files to be attached to other files | * Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat) |
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| * Various initiatives: http://samirdas.github.io/Data_sharing.html#/ | |
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| * Mixed head models: * Project to templates (scouts or source maps) * Create scout form maximum doesn't work (menu Sources > Max value) * Display in MRI doesn't work * Smooth display: do not smooth subcortical structures * Export as .nii volume: doesn't work * Project individual volume grids on a template |
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| * Finish dipole scanning (allow the tab to control multiple figures separately) * Dipole fitting: We will not implement non-linear fits, recommended use of dense volume grids |
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| * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates | |
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| * Create scout form maximum: Not available yet for mixed/volume head model. | |
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| * Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST) | * Inner and outer skull surfaces generator from FieldTrip (needs SPM) |
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| * Compute unconstrained and then project on the normal ? * Difference and stat should be: norm(A) - norm(B) |
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| * When deploying to other conditions: Apply destination SSP (NoiseCov = SSP . NoiseCov . SSP' ) | |
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| * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise) | |
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| * EEG Source modeling: Manage references and bipolar montages properly (maybe not necessary) * MEG source modeling: Do reconstruction only for a subset of sensors for estimating dipoles? * Processes compute head model and sources: Additional option to set the file comment |
* Beamformers from FieldTrip (LCMV, SAM) |
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| * Display volume scouts and surface scouts at the same time | |
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| * Project all sub-cortical structures to default anatomy | * MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256) * Project all sub-cortical structures to default anatomy (check code from Denis S) * BrainVISA: Add support for MarsAtlas (Guillaume A) * Add cerebellum to default model generated with "Import FS anatomy" * Import MRIs with different resolutions: re-interpolate automatically * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m) |
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| * Project scouts betweens subjects and between hemispheres | |
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| * Menu head model > Copy to other conditions/subjects (check if applicable first) * Generate mixed density surfaces * Optimize computation interpolation MRI-surface (tess_tri_interp) * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix * Major bug when importing surfaces for an MRI that was re-oriented manually * Smooth surface: Fix little spikes due to irregularities in the mesh * Add eyes models to attract eye activity * tess_mrimask: Not robust enough to major holes in the brain == ECOG/SEEG == |
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| * Generate mixed density surfaces * Import / registration: * Major bug when importing surfaces for an MRI that was re-oriented manually * Use mid-gray instead of pial surface? * Smooth surface: Fix little spikes to irregularities in the mesh * Menu head model > Copy to other conditions/subjects (check if applicable first) * Add cerebellum to default model generated with "Import FS anatomy" * Add eyes models to attract eye activity |
* Import/export electrodes positions in MNI/SCS/MRI coordinates * Display SEEG+ECOG contacts at the same time * Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned |
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| * ANOVA: Use LENA functions | * ANOVA: * Use LENA functions(?) |
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| * Permutation tests: * t-test only (wilcoxon? sign-test?): paired, equal var, unequal var * http://www.adscience.fr/uploads/ckfiles/files/html_files/StatEL/statel_wilcoxon.htm * http://www.mathworks.fr/fr/help/stats/signrank.html * Less powerful than t-tests * nb permutations ~ 1000 * maximum statistic over "time" or "time and space" * Permutations / clustering: cf fieldtrip * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock * http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq * Maris, Eric & Oostenveld, Robert. "Nonparametric statistical testing of EEG-and MEG-data." * Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points<<BR>> => Process that creates a static representation of a temporal window * t-test on volume sources * Paired t-test on unconstrained sources: (convert to flat + Z-score) => AnneSo * Question of Gaussianity of the samples: take a subset of samples + Kolmogorov-Smirnov / Shapiro-Wilk test * http://fr.wikipedia.org/wiki/Test_de_Shapiro-Wilk * http://stats.stackexchange.com/questions/362/what-is-the-difference-between-the-shapiro-wilk-test-of-normality-and-the-kolmog * http://www.mathworks.fr/fr/help/symbolic/mupad_ug/perform-shapiro-wilk-test.html * http://www.mathworks.fr/fr/help/symbolic/mupad_ref/stats-swgoft.html * http://stackoverflow.com/questions/14383115/shapiro-wilk-test-in-matlab * Create icons for Stat/PAC, Stat/Sprectrum, etc. * One sample t-test across subjects |
* New process to test for Gaussianity using swtest * PLS: Partial Least Squares * Simulate recordings with specific properties, for stat validation * Quality control before statistics, on condition averages across subjects:<<BR>>mean(baseline)/std(baseline): shows bad subject quickly. * Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter |
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| * Finish MINC/CIVET integration (finir lecture MINC2: P Bellec) * Send email to CIVET mailing list when done * FieldTrip structures: In / Out (see fieldtrip/utilities/ft_datatype_*) |
* 4D file format: * Reference gradiometers: Keep the orientation of the first or second coil? * Reference gradiometers: Add the sensor definition from coil_def.dat * Validate with phatom recordings that noise compensation is properly taken into account * References at too far from the head sensors in Marseille 4D system * The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct |
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| * Selection of conditions in script mode | |
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| * Allow epoched files with recordings saved in external files (now external files implies continuous recordings) | * Allow epoched files with recordings saved in external files |
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| * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports. * Use new Matlab functions readtable/writetable (2006b): for Excel and text files |
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| * Document iEEG in "What's new" * Rewrite basic 12+3 tutorials: group in one series * Illustrate 2D Layout * Illustrate unconstrained sources |
* Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip * Reference tutorials on Google scholar + ResearchGate |
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| * Add Help buttons and menus (in popups, dialog windows...) => Links to the website. * Publication list: Fold by years |
* Update the list of features and link in the Introduction page |
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| * EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough) | |
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| * Auditory: Extend to MNE/EEGLAB/SPM * Auditory: Finish scripts |
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| * MEG connectome * Scrambled faces (SPM/MNE-Python) * Describe all the processes * Statistics |
* MEG steady-state / high-gamma visual * Intra-cranial recordings * MEG connectome (impossible without the head shapes) |
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| * Intra-cranial recordings (Average ref by groups using Comment field) | |
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| * SSP: Create projector from any topography figure (right-click > Create SSP) | |
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| * First steps: Brainstorm preferences * First steps: Temporary folder * Exploration: Clusters * Headmodel: explain the fields + how to get the constrained leadfield * Sources: Model evaluation (by simulating recordings) * Sources: Theshold min. size (not documented yet) |
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| * Modify a structure manually: Export to Matlab/Import from Matlab | * Scripting: Modify a structure manually: Export to Matlab/Import from Matlab * Scripting: File manipulation: file_short, file_fullpath, in_bst_*... * Detect bad channels: Peak-to-peak * Script tutorials: ask what folder contains the tutorial datasets |
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| * Reference tutorials on Google scholar * Play videos on wiki with <video> tag (save videos in .ogg) |
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| * Workshops: * Create scouts doesn't work: scout created on the other side of the brain * Import anatomy folder: Out of memory on Win 32bits (restart Matlab) * Compute head model: Out of memory on Win 32bits * Bandpass filter: Out of memory (Auditory workshop) * Bug workshop Michael (Mint 12/gnome3/linux 3.0.0-12, KWin/Mutter/Compiz) * Cannot import two .ds folders at once * Colors inverted in the PSD/TF plots (power vs. log) * Cannot type the name of a channel in "Detect ECG" * Image viewer: Difficult to get to 100% |
* Screen capture: * Bug on Win8/Win10: doesn't capture the correct part of the screen * Window managers with fading effect: captures the top window * Image viewer: * Difficult to get to 100% * Buggy on some systems * 2DLayout: * (TF) Images are too far apart with EEG 20 channels * (TF) Units are weird with % values * (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling * (time series) Sometimes the lines are not visible * (time series) Does not work when DC offset is not removed * Progress bar: * Doesn't close properly on some Linux systems * Focus requests change workspace when processing constantly (Linux systems) * MacOS bugs: * Buttons {Yes,No,Cancel} listed backwards * Record tab: Text of epoch number is too big * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10 * Matlab bugs: * Interface looks small on screens with very high resolutions: Reduce the resolution * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file) * Edit scout in MRI: small modifications cause huge increase of the scout size |
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| * Smooth TF windows that contain multiple plots * Record tab: Text of epoch number is too big on MacOS * in_bst_data_multi: If trials have different sizes, output is random (the one of the first file) * tree_dependencies: sources files, reprojected on default anatomy; If based on data files that are bad trials, they should be ignored by tree_dependencies, and they are not * Image viewer has some bugs on some systems * Screen capture when there is a fading effect in the window manager: captures the window * Close figure with coherence results should hide the "frequency" slider * Edit scout in MRI: small modifications cause huge increase of the scout size * Reports: Text size is too small with Java 1.5 (2006b-2007a) * Optimize MRI viewer with patch() instead of image() * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call * 2DLayout (time series): * Sometimes the lines are not visible * Does not work when DC offset is not removed * 2DLayout (TF): Images are too far apart with EEG 20 channels * Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG. |
* Change of default anatomy does not reset the interpolation matrices in all the subjects. * After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template. |
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| * mri2scs: convert arguments to meters * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b) |
* Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b) |
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| * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow) | * Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow) |
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| * Line smoothing / anti-aliasing (time series figures) | |
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| * Replace handle "0" with bst_get('groot') * At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame) |
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| * in_bst_results (isFull=1): DataFile should be relative |
What's next
A roadmap to the future developments of Brainstorm.
Contents
Current topics
Source modeling
- Implementation of a new unified minimum norm/beamformer framework (work in progress)
Documentation
- Standard workflows for different types of data and experiments (work in progress)
Cross-validation with MNE and FieldTrip:
http://martinos.org/mne/dev/auto_tutorials/plot_brainstorm_auditory.html
Functional connectivity
- Significance thresholding of the connectivity matrices (not started)
Computation
- Removing the dependence to the Java interface to run in headless mode (not started)
Recordings
- 2D topographies:
- Nicer topographies with circle around 2DDisc (similar to EEGLAB plots)
Standardized plots (using FieldTrip .lay files?)
- Aligned on the midline at least
- Contour lines sometimes messed up with Elekta recordings
- Make the surface on which the values are interpolated simpler
- MEG/EEG registration: Apply the same transformation to multiple runs
- Montages:
- Separators (" : MLC11" already works, could be just " : "), should add an empty space.
- 2DLayout:
- Use the same standard positions, too much space between sensors (Recordings + TF)
- Overlay multiple conditions
RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
- Same shortcuts as the raw file viewer (right-click + move for gain)
- Add support for montages
- RAW file viewer:
- Show easily the maximum value at the current time point
- Pre-load next page of recordings
- Events: Change the category of a selected event easily, instead of deleting/marking new
- Events: advanced process for recombining.
Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
Interface
- Start Brainstorm without Java (-nodesktop)
Allow FieldTrip functions in compiled version
Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly
- Colormaps:
- Allow brightness/contrast manipulations on the custom colormaps
- Create a colormap similar to MNE, where extrema are bright
- Global colormap max: Should get the maximum across all the open files
- Open new figures as tab (docked in the Figures window)
- Copy figures to clipboard (with the screencapture function)
- Removing all the CTRL and SHIFT in the keyboard shortcuts
- Display warning before opening files that are too big
- Smooth display from figure_image (ERPimage, raster plot...)
Connectivity
- Thresholding the connectivity matrices
- Stat tests on connectivity measures
- Connectivity on unconstrained sources: how to group the three orientations?
Review by Jan-Mathijs: http://journal.frontiersin.org/article/10.3389/fnsys.2015.00175/full
- Connectivity based on band limited power (Sylvain):
- Compute Hilbert/Bandpass + correlation of the envelopes
- Bandpass envelopes before computing correlations?
- Compute Hilbert(sensors) and then project to source space?
- Graph view:
- Does not display negative values correctly (correlation or difference of coherence)
- Re-write using pure Matlab code and smoothed graphics
- Fixed scales for intensity sliders
- Text bigger
- Too much data in appdata
- Fixed scales for intensity sliders
- Add "=" shortcut for having graphs with similar configurations
- Disable zoom in one region (serious bugs)
- NxN on sensors: does not place the sensors correctly in space
- Coherence:
- Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
- Granger:
- Crashes sometimes: improve stability
- Re-write and optimize code
- Add progress bar
- PLV:
- Add p-values
- Remove evoked
- Optimize code
- Add time integration
- Unconstrained sources
- PAC:
- Add input TF , to disconnect TF decomposition and PAC computation (Peter)
- Refine frequency vector of low frequencies
- How many central frequencies to use in bst_pac?
- Change filters: no chirplet functions
- bst_freqfilter: Use nfcomponents like in bst_pac
- Esther recommended a larger frequency binning of the PAC estimation
- PAC maps: Display all sensors at once (like TF and DynamicPAC)
- Time-resolved correlation/coherence: Display as time bands
- Other metrics:
- Coherence by bands: bst_coherence_band_welch.m
- Granger by bands: bst_granger_band.m
- Inter-trial coherence
Tutorial coherence [1xN] : Reproduce FieldTrip results?
Connect NxN: Display as time series > Display warning before trying to open too many signals
Processes
- PLS:
- meg-pls dot weebly dot com
Krishnan 2011: http://www.ncbi.nlm.nih.gov/pubmed/20656037
Cheung 2015: http://www.sciencedirect.com/science/article/pii/S1053811915007648
McIntosh 2012: http://www.ncbi.nlm.nih.gov/pubmed/22804773
McIntosh 2004: http://www.ncbi.nlm.nih.gov/pubmed/15501095
- Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow
- ICA:
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
- Export IC time series (and then compute their spectrum): solves the problem above
Comparison JADE/Infomax:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135- Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB
Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )
Student Carl Leichter detailed this in his thesis- S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
- Display of spectrum for components (PSD/FFT)
- Use FastICA (algo crashing)
- Understand why EEG/Epilepsy tutorial data crashes if we don't limit the number of components
- Add components preselection: Correlation with EOG/ECG
- Import ICA matrices available in EEGLAB .set files
EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm
(http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA)
- Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
- Allow processes in Python and Java
- SSP:
Display warning if changing the ChannelFlag while there is a Projector applied
Show where the attenuation is projected:
(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
- Bandpass:
- Offer option: bst_bandpass_fft / bst_bandpass_filter
- Rewrite without the forced low-pass filter at Fs/3
- Show warning when using inappropriate high-pass filter (precision too high)
- Use FIR filter
- Spectral flattening (John):
- ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis
- PSD:
- Rewrite to have the same input as coherence (frequency resolution instead of window length)
- Use the progress bar
Remove line noise: http://www.nitrc.org/projects/cleanline
- Band-limited power envelope
- Reports:
- Save as HTML / PDF
- Pipeline editor:
- Add loops over subjects/conditions/trial groups
- Time-frequency:
- Multi-tapers
Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
- Bug: Display logs as negative
- Bug: 3D figures: Colormaps with "log" option doesn't work
- Bug: Difference of power displayed in log: problems (Soheila)
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- TF scouts: should display average of TF maps
- Impossible to keep complex values for unconstrained sources
- Pad short epochs with zero values for getting lower frequencies
- Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
- Extend clusters tab to display of TF to overlay TF signals (Svet)
- When normalizing with baseline: Propagate with the edge effects marked in TFmask
- Artifact detection:
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
- Co-registration of MEG runs:
- SSP: Group projectors coming from different files
- Finish validation of the method
- Apply to continuous recordings for correcting head movements
- Resample continuous files
- Other processes:
- Moving average
- Max
- Median
- Significance test (Dimitrios, Leo)
- Spatial smoothing: check / document parameters
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
- Optical flow
- Simulation:
Fix units in simulation processes => no *1e-9 in "simulate recordings"
- Use "add noise" process from Hui-Ling (in Work/Dev/Divers)
- Use field process field "Group" to separate Input/Processing/Output options
- Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd
Database
- Sort files by comment
- MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
- Matrix files: Allow to be dependent from other files
- Add notes in the folders (text files, visible as nodes in the tree)
- Screen captures: save straight to the database
- Rename multiple files
- Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)
Distributed computing
Options from FieldTrip:
Loose collection of computers: https://github.com/fieldtrip/fieldtrip/tree/master/peer
Alternative, with less limitations: http://research.cs.wisc.edu/htcondor/
Single multicore machine: https://github.com/fieldtrip/fieldtrip/tree/master/engine
Batch system: https://github.com/fieldtrip/fieldtrip/tree/master/qsub
Documentation: http://fieldtrip.fcdonders.nl/faq#distributed_computing_with_fieldtrip_and_matlab
Various initiatives: http://samirdas.github.io/Data_sharing.html#/
Source modeling
- Mixed head models:
- Project to templates (scouts or source maps)
Create scout form maximum doesn't work (menu Sources > Max value)
- Display in MRI doesn't work
- Smooth display: do not smooth subcortical structures
- Export as .nii volume: doesn't work
- Project individual volume grids on a template
- Dipoles:
- panel_dipoles: Doesn't work with multiple figures
- Panel Get coordinates: Add button "find maximum"
- Stenroos 2014 paper: Include the following methods
Inner and outer skull surfaces generator from FieldTrip (needs SPM)
- Nolte corrected-sphere model (good model re:Alex)
- Fast BEM models
- Visualize Beamformer results:
- Read CTF SAM .svl
- Display as layers in the MRI viewer
- Unconstrained sources:
- Stat and connectivity: what to do? (re-send email John+Sylvain)
- Overlapping spheres: improve the estimation of the spheres for the frontal lobes
- Volume grid:
- Test volume sources with all the subsequent processes (timefreq, stat...)
- Optimize: 3D display (better than 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
- Magnetic extrapolation: Do the same thing with EEG
- Noise covariance matrix:
- Display with figure_image()
- Storage of multiple noise covariance matrices (just like the head models)
- Always save as full, then at inversion time, we can decide between full, heteroskedastic (diagonal) or homoskedastic (i.i.d, scalar)
Problem of having inividual trials + averages in the condition => Display warning or not?
- Save nAvg in noisecov file, to make it easier to scale to other recordings
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Calculate ImagingKernel * Gain for a scout
Beamformers from FieldTrip (LCMV, SAM)
- Time-frequency beamformers:
- Band-pass everything in different frequency bands + Source estimation + TF
- Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
- Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
- BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
- Hui-Ling beamformers:
- More explanations about what is in NAI and Spatial filters
Explain that is this is better to study effects extended in time (Ntime > Nsensors)
- Group LCMV+MCB
- Condition LEFT median nerve: very bad results
Menu Sources > Simulate recordings:
- Do not close the 3D figures after generating a new file
- Add a process equivalent to this menu
Anatomy
MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)
- Project all sub-cortical structures to default anatomy (check code from Denis S)
BrainVISA: Add support for MarsAtlas (Guillaume A)
- Add cerebellum to default model generated with "Import FS anatomy"
- Import MRIs with different resolutions: re-interpolate automatically
- Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
- Warping: Scale option has to be fixed, it is currently very unstable
- Scouts:
- Display edges in the middle of the faces instead of the vertices
- Display scouts in a tree: hemisphere, region, subregion
- Downsample to atlas: allow on timefreq/connect files
- Sort scouts by region in process options
Menu head model > Copy to other conditions/subjects (check if applicable first)
- Generate mixed density surfaces
- Optimize computation interpolation MRI-surface (tess_tri_interp)
- Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
- Major bug when importing surfaces for an MRI that was re-oriented manually
- Smooth surface: Fix little spikes due to irregularities in the mesh
- Add eyes models to attract eye activity
- tess_mrimask: Not robust enough to major holes in the brain
ECOG/SEEG
- Co-register MRI and CT for electrodes marking in the MRI Viewer
- Import/export electrodes positions in MNI/SCS/MRI coordinates
- Display SEEG+ECOG contacts at the same time
Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
Statistics
- ANOVA:
- Use LENA functions(?)
- Output = 1 file per effect, all grouped in a node "ANOVA"
- Display several ANOVA maps (from several files) on one single figure, using a "graphic accumulator", towards which one can send any type of graphic object
- New process to test for Gaussianity using swtest
- PLS: Partial Least Squares
- Simulate recordings with specific properties, for stat validation
Quality control before statistics, on condition averages across subjects:
mean(baseline)/std(baseline): shows bad subject quickly.Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
Input / output
- 4D file format:
- Reference gradiometers: Keep the orientation of the first or second coil?
- Reference gradiometers: Add the sensor definition from coil_def.dat
- Validate with phatom recordings that noise compensation is properly taken into account
- References at too far from the head sensors in Marseille 4D system
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- EEG File formats:
EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- BCI2000 Input (via EEGLAB plugin)
- EEGLAB import:
- Support for binary AND epoched files (now it's one or the other)
- Allow epoched files with recordings saved in external files
- BST-BIN: Add compression
- Review raw on all the file formats (ASCII EEG and Cartool missing)
- gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
- Use new Matlab functions readtable/writetable (2006b): for Excel and text files
Distribution & documentation
Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip
Reference tutorials on Google scholar + ResearchGate
- Cleaning threads on the forum
- Update the list of features and link in the Introduction page
- Finish existing tutorials:
- EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough)
- Dipoles
- Group MEM/Epilepsy + Epilepsy tutorials
- New tutorials:
- MEG steady-state / high-gamma visual
- Intra-cranial recordings
- MEG connectome (impossible without the head shapes)
- Coherence (cortico-muscular ?)
- Co-register MEG runs (Beth)
- Missing in the introduction tutorials:
SSP: Create projector from any topography figure (right-click > Create SSP)
- Volume scouts
- Time-frequency: Description of "log freq scale" option
- Scripting: Modify a structure manually: Export to Matlab/Import from Matlab
- Scripting: File manipulation: file_short, file_fullpath, in_bst_*...
- Detect bad channels: Peak-to-peak
- Script tutorials: ask what folder contains the tutorial datasets
- Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
- Missing in page "Cite Brainstorm": Add all the methods used in the software
Current bugs
- Screen capture:
- Bug on Win8/Win10: doesn't capture the correct part of the screen
- Window managers with fading effect: captures the top window
- Image viewer:
- Difficult to get to 100%
- Buggy on some systems
- 2DLayout:
- (TF) Images are too far apart with EEG 20 channels
- (TF) Units are weird with % values
- (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
- (time series) Sometimes the lines are not visible
- (time series) Does not work when DC offset is not removed
- Progress bar:
- Doesn't close properly on some Linux systems
- Focus requests change workspace when processing constantly (Linux systems)
- MacOS bugs:
- Buttons {Yes,No,Cancel} listed backwards
- Record tab: Text of epoch number is too big
- Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
- Matlab bugs:
- Interface looks small on screens with very high resolutions: Reduce the resolution
- Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG
- in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
- Edit scout in MRI: small modifications cause huge increase of the scout size
- Canolty maps computation: Fix progress bar
- Change of default anatomy does not reset the interpolation matrices in all the subjects.
- After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template.
Geeky programming details
- Hide Java panels instead of deleting them
- Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
- bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
- Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow)
- Optimize bst_get:
- Now study and subject have necessarily the same folder name
- Replace big switch with separate functions
- Progress bar:
- Add different levels (to handle sub-processes)
- Make work correctly with RAW on resting tutorial
- Uniformize calls in bst_process/Run
- Add a "Cancel" button
- Fix all the 'todo' blocks in the code
- Error message: Add a link to report directly the bug on the forum