Differences between revisions 21 and 80 (spanning 59 versions)

What's next

A roadmap to the future developments of Brainstorm.

Current topics

Functionnal connectivity

Integration of different metrics to study the brain connectivity:
Correlation, coherence, Granger causality, phase locking value
Development of new ways to represent the connectivity between sensors or brain regions

EEG / epilepsy / intra-cranial recordings

New tools for exploring EEG recordings (custom montages, faster viewer)
Full EEG/epilepsy online tutorial
Editing the position of intracranial electrodes in the MRI viewer

Source modeling

Computation of equivalent current dipoles
Beamformers

Large scale analysis

Parallel processing: Reduce the computation times using the parallel processing toolbox
Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters

Recordings

RAW file viewer:
- Pre-load next page of recordings
- Allow multiple RAW windows(columns display)
- Screen setups: save configuration of windows
- Time scale: define in fixed s/mm (like the CTF tools)
- Secondary windows: display length of time selection
- If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
- Documentation: Add definition of bad segments
- Set the amplitude scale for the time series
- CTRL+S : Save modifications
Intracranial electrodes: Define and display in the MRI viewer + 3D figures
RAW processing:
- Make it work for all the file formats (at least bandpass filter + sin removal)
- Events: advanced process for recombining. Example: http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
Colormaps:
- Define manually minimum => 3 options: [0,max], [-max,max], [min,max]
- Create a colormap similar to MNE, where extrema are bright
- Grey out the portion of the colorbars not displayed because of the threshold
EEG display:
- bst_selections: Add user defined combinations of sensors (eg. "double banana" for EEG)
- Define custom montage
- Re-reference recordings
Import data:
- Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files)
NIRS:
- Add new data type
- Display of sensors by pairs oxy/deoxy (red/blue), overlaid
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
2D Layout for multiple conditions

Connectivity

Figures: interaction with sensor selection / scouts selections
Display NxN as 1xN
Adapt colormaps for correlation (min and max properties)
PLV: Add a time integration
Correlation with delays?
Work on progress bars
Circle plot: Display Neuromag sensors
Event-related coherence?

Processes

Time-frequency:
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- Scouts values for timefreq on surfaces
- How to combine 3 orientations for unconstrained sources
- Display logs as negative
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- Smooth display of TF/PAC maps (option)
- TF scouts: should display average of TF maps
Artifact detection:
- Detection of bad segments in the RAW files
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
Distributed processing: Brainstorm that can run without JAVA
SSP:
- Display warning if changing the ChannelFlag while there is a Projector applied
- When processing multiple files: waitbar is not behaving well
- Improve interface for SSP on imported recordings
- Define SSP from one time point
- Show where the attenuation is projected:
  (sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
Average:
- Remember how many trials were used per channel
- Save standard deviation
- Display standard deviation as a halo around the time series
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
Current Source Density (CSD) => Ghislaine
http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html
Other processes:
- Detrending
- 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
Spectrum figure: use bst_selection

Database

MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
Group matrix files => allow to process matrix files by trial types
Add notes in the folders (text files, visible as nodes in the tree)
Screen captures: save straight to the database

Source modeling

Dipole fitting
Visualize Beamformer results (contact Zainab Fatima):
- Read CTF SAM .svl
- Create new file type in the database
- Display as layers in the MRI viewer
Unconstrained sources:
- Compute unconstrained and then project on the normal ?
- Difference and stat should be: norm(A) - norm(B)
- 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:
- Scouts 3D
- Test volume sources with all the subsequent processes (timefreq, stat...)
- Optimize: 3D display (better that 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
Magnetic extrapolation:
- Do the same thing with EEG
Noise covariance matrix:
- 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
- When deploying to other conditions: Apply destination SSP (NoiseCov = SSP . NoiseCov . SSP' )
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise)
Calculate ImagingKernel * Gain for a scout

Anatomy

Scouts:
- Mix constrained/unconstrained/volume sources, using the "Source model" atlas
- Display edges in the middle of the faces instead of the vertices
- Project scouts betweens subjects and between hemispheres
- Display scouts in a tree: hemisphere, region, subregion
- Downsample to atlas: allow on timefreq/connect files
- Sort scouts by region in process options
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?

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
Permutation tests:
- t-test only (wilcoxon? sign-test?): paired, equal var, unequal var
- 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
Threshold in time: keep only the regions that are significative for contiguous blocks of time, or over a certain number of time points
=> Process that creates a static representation of a temporal window
t-test on volume sources
Create icons for Stat/PAC, Stat/Sprectrum, etc.
One sample t-test across subjects

Input / output

EEG File formats:
- EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
FieldTrip structures: In / Out
BCI2000 Input (via EEGLAB plugin)
Export TF maps to SPM / volumes
EEGLAB import: Selection of conditions in script mode

Distribution & documentation

Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
Introduction tutorials:
- Processes: Describe all the processes
- Clusters
- First steps: Brainstorm preferences
- Headmodel: explain the fields + how to get the constrained leadfield
- Sources: Modelized data
- Sources: theshold min. size (not documented yet)
- Import raw recordings: Add "detect bad trials/channels" in the pipeline
- Temporary folder
Advanced tutorials:
- EEG (How to import an EEG cap)
- Epilepsy / spike analysis

Current bugs

Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
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 for reports never works: Find another solution
Close figure with coherence results should hide the "frequency" slider

Geeky programming details

Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
Hide Java panels instead of deleting them
mri2scs: convert arguments to meters
bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
Shared kernels: do the "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
Line smoothing / anti-aliasing (time series figures)
Optimize reload time

-  ⇤ ← Revision 21 as of 2012-01-10 21:18:01 → 
  Size: 11277
  Editor: wpa162144
  Comment:
+   ← Revision 80 as of 2014-01-07 21:47:48 → ⇥
  Size: 10634
  Editor: agrippa
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
-== Next six months ==
==== Data acquisition ====
 * Improve the acquisition of the head points and the registration MEG / MRI

==== Pre-processing ====
 * Extend processing of continuous CTF files to all file formats
 * Continuous viewer: Many small improvements to the usability of its interface
 * Improve detection and correction of artifacts with SSP
 * Co-registration of several MEG runs on one single head position
 * Make all the main operations available in the pipeline editor

==== File formats ====
 * MRI: MINC
 * EEG: Stellate
 * EEG: Brain Products / !BrainAmp
 * Read and display NIRS recordings
 * CTF SAM Beamformer results
+== Current topics ==
-Line 23:
+Line 6:
- * Implementation of methods developed at USC
+ * Integration of different metrics to study the brain connectivity: <<BR>>Correlation, coherence, Granger causality, phase locking value
 * Development of new ways to represent the connectivity between sensors or brain regions

==== EEG / epilepsy / intra-cranial recordings ====
 * New tools for exploring EEG recordings (custom montages, faster viewer)
 * Full EEG/epilepsy online tutorial
 * Editing the position of intracranial electrodes in the MRI viewer

==== Source modeling ====
 * Computation of equivalent current dipoles
 * Beamformers

==== Large scale analysis ====
 * Parallel processing: Reduce the computation times using the parallel processing toolbox
 * Distributed processing: Integrate tools for sending Brainstorm processes on computation clusters
-Line 29:
+Line 26:
-  * Buttons for changing scales (time + amplitude)
  * Add tooltips to all the buttons / shortcuts
  * Adding events using configurable shortcuts (CTRL+number)
+  * Pre-load next page of recordings
  * Allow multiple RAW windows(columns display)
  * Screen setups: save configuration of windows
  * Time scale: define in fixed s/mm (like the CTF tools)
  * Secondary windows: display length of time selection
-Line 34:
+Line 33:
+  * Set the amplitude scale for the time series
  * CTRL+S : Save modifications
 * Intracranial electrodes: Define and display in the MRI viewer + 3D figures
-Line 35:
+Line 37:
-  * Process correctly CTF files saved without the 3rd order grad correction (apply correction before)
  * Allow to overwrite RAW files (but with a HUGE warning)
  * Update file definition + events if time changes (ex: resample)
  * Make it work for the file formats
 * Homogenize a selection of several subjects/conditions
  * Popup menu when more than one study selected
  * Creation of a common channel file (match channels by names, not by order)
  * Register MEG runs (recompute fields for a different set of sensors, MEGCoregister from old brainstorm)
 * bst_selections:
  * Add user defined combinations of sensors (eg. "double banana" for EEG)
  * Use this to produce "inversed polarity" displayes too (useful in EEG)
  * Standard setups for al the EEG caps
 * Intracranial electrodes:
  * Display in the MRI viewer
  * Different data type
  * Display time series
 * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
+  * Make it work for all the file formats (at least bandpass filter + sin removal)
  * Events: advanced process for recombining. Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
 * Colormaps:
  * Define manually minimum => 3 options: [0,max], [-max,max], [min,max]
  * Create a colormap similar to MNE, where extrema are bright
  * Grey out the portion of the colorbars not displayed because of the threshold
 * EEG display:<<BR>>
  * bst_selections: Add user defined combinations of sensors (eg. "double banana" for EEG)
  * Define custom montage
  * Re-reference recordings
 * Import data:
  * Save properties "baseline" and "resample" at the level of the protocol (to re-use for all the files)
 * NIRS:
  * Add new data type
  * Display of sensors by pairs oxy/deoxy (red/blue), overlaid
 * 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
 * 2D Layout for multiple conditions

== Connectivity ==
 * Figures: interaction with sensor selection / scouts selections
 * Display NxN as 1xN
 * Adapt colormaps for correlation (min and max properties)
 * PLV: Add a time integration
 * Correlation with delays?
 * Work on progress bars
 * Circle plot: Display Neuromag sensors
 * Event-related coherence?
-Line 54:
+Line 68:
+ * Time-frequency:
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * Scouts values for timefreq on surfaces
  * How to combine 3 orientations for unconstrained sources
  * Display logs as negative
  * 2D Layout in spectrum
  * Make much faster and more memory efficient (C functions coded by Matti ?)
  * Smooth display of TF/PAC maps (option)
  * TF scouts: should display average of TF maps
 * Artifact detection:
  * Detection of bad segments in the RAW files
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
 * Distributed processing: Brainstorm that can run without JAVA
-Line 55:
+Line 83:
-  * Make SSP projections dynamic, and keep the full list instead of always them combining them
  * Take the bad channels in account in the application of the SSP
  * Refresh display after changing the list of bad channels (imported files + raw) so the SSP are applied correctly
  * When processing multiple files: waitbar is all messed up
  * Tune parameters for the automatic detection of heartbeats and eye blinks
  * Write documentation
 * Complete processing pipeline:
  * Import + pre-process
  * Sources / head model / noise covariance
  * Project sources
  * Do not generate errors, stay silent and generate a report log that is shown at the end
  * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
+  * Display warning if changing the !ChannelFlag while there is a Projector applied
  * When processing multiple files: waitbar is not behaving well
  * Improve interface for SSP on imported recordings
  * Define SSP from one time point
  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
-Line 69:
+Line 90:
-  * By subject AND condition

 * Time-frequency:
  * Write script for timefreq tutorial
  * Make much faster and more memory efficient (C functions coded by Matti ?)
  * Power spectrum: computation (FFT/welch, or average of TF) + display(f/Power, 2DLayout)
  * Display stat computed on time-frequency data
  * Display TF maps separately for the two gradiometers (if not: overlap)
  * Source reconstruction by frequency bands
  * Scouts on surface / time-freq
 * Process selection interface:
  * Do not reload the list a each display, but once when starting Brainstorm
  * Popup menus: Add a "Process" menu with all the available processes
  * Bug when redimensioning window (with more than one process)
  * isAvgRef: warning quand process necessite des donnees en AVG REF en entree
  * Save "freqband" option when edited from custom processes
+  * Save standard deviation
  * Display standard deviation as a halo around the time series
 * 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
 * Current Source Density (CSD) => Ghislaine<<BR>>http://psychophysiology.cpmc.columbia.edu/software/CSDtoolbox/index.html
-Line 86:
+Line 98:
+  * Detrending
-Line 87:
+Line 100:
-  * Remove linear trend
  * Power line removal
  * Bug: gradnorm crashes with bad channels
+  * Max
  * Median
  * Significance test (Dimitrios, Leo)
-Line 91:
+Line 104:
-  * Sinusoid removal: fix new function
-Line 93:
+Line 105:
+ * Optical flow
 * Spectrum figure: use bst_selection
-Line 96:
+Line 110:
- * GUI: Save configuration of windows (per protocol)
+ * Group matrix files => allow to process matrix files by trial types
-Line 100:
+Line 114:
+ * Screen captures: save straight to the database
-Line 101:
+Line 117:
+ * Dipole fitting
-Line 107:
+Line 124:
-  * Define as default
  * Check all the processes
-Line 110:
+Line 125:
+  * Stat and connectivity: what to do? (re-send email John+Sylvain)
-Line 116:
+Line 132:
-  * Optimize: grid_interp_mri
-Line 119:
+Line 134:
-  * Optimize bst_extrapm.m, add waitbar
  * Use the noise covariance from the database instead of recomputing it
 * Project sources:
  * Adapt smooth factor to the number of vertices
  * Number of neighbors to consider = average number of neighbors in the target mesh.
  * Compute by small time blocks
-Line 126:
+Line 135:
+  * 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?
-Line 130:
+Line 142:
+ * Calculate !ImagingKernel * Gain for a scout
-Line 132:
+Line 145:
- * BEM surfaces:
  * Fix the bumps at the back of the head
  * Surface edges: same color as the surface when color was changed
+ * Scouts:
  * Mix constrained/unconstrained/volume sources, using the "Source model" atlas
  * Display edges in the middle of the faces instead of the vertices
  * Project scouts betweens subjects and between hemispheres
  * Display scouts in a tree: hemisphere, region, subregion
  * Downsample to atlas: allow on timefreq/connect files
  * Sort scouts by region in process options
 * Generate mixed density surfaces
-Line 136:
+Line 154:
-  * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
  * Auto-reorientation of MRI  after selected NAS / LPA / RPA
-Line 139:
+Line 155:
- * ICBM brain
  * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab
  * ICBM average surfaces + atlas
  * Using CIVET pipeline for extracting surfaces
 * Atlas:
  * Use BrainVISA / !FreeSurfer labeling automatically when importing cortex surface
  * Finalize Brodmann scouts
  * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND
 * Clustering cortex: Dimitrios, David, Yu-Teng
+ * Use mid-gray instead of pial surface?
-Line 150:
+Line 158:
- * Stat on scouts / clusters / "matrix"
-Line 162:
+Line 169:
+ * t-test on volume sources
 * Create icons for Stat/PAC, Stat/Sprectrum, etc.
 * One sample t-test across subjects
-Line 165:
+Line 175:
-  * Stellate
  * !BrainVision / !BrainAmp: Get functions from EEGLAB
  * Nihon Kohden
  * EDF+
-Line 170:
+Line 176:
-  * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler
-Line 172:
+Line 177:
- * Other file formats
  * MEG160  (KIT)
  * CTF: Read STIM channel and generate !MarkerFile
  * EEGLAB: Apply ICA matrices, get number of trials for AVG files
  * !FieldTrip structures: In / Out
  * Output for all the channel file formats
 * Define scouts from SPM / Analyze 3D masks
 * Files > 2Gb: display warnings
+ * !FieldTrip structures: In / Out
 * BCI2000 Input (via EEGLAB plugin)
 * Export TF maps to SPM / volumes
 * EEGLAB import: Selection of conditions in script mode
-Line 182:
+Line 183:
- * Version with big fonts for live demos
 Line 184:
- * List of all the keyboard and mouse shortcuts
 * Send emails to registered users to anounce major improvements
 * Script tutorials:
  * Update them to reflect all the recent changes
  * Script for the time-frequency computation
-Line 190:
+Line 185:
-  * Estimate time to complete each tutorial
+  * Processes: Describe all the processes
-Line 192:
+Line 187:
-  * Anatomy: Segmentation with !FreeSurfer
-Line 195:
+Line 189:
-  * Coordinate sytems: How to convert between the different coordinates systems in scripts
-Line 198:
+Line 191:
-  * Scouts: Atlases of Tzourio-Mazoyer and Brodman
  * Processes: Describe all the processes
  * Processes: How to write your own processes (user folder for processes)
  * Processes: Processing RAW files
-Line 203:
+Line 192:
+  * Temporary folder
-Line 204:
+Line 194:
-  * MNE sample dataset
-Line 206:
+Line 195:
-  * MRI segmentation with !FreeSurfer => David Wheland
  * How to make and compress a movie (Brainstorm + !VirtualDub + XVid)
 * Display the "What's new" page after downloading new version of brainstorm
 * Ask users to send their channel files, align on Colin, distribute
+  * Epilepsy / spike analysis

== Current bugs ==
 * Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
 * 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 for reports never works: Find another solution
 * Close figure with coherence results should hide the "frequency" slider
-Line 212:
+Line 206:
- * OpenGL options: {none, software, hardware}
 * Bug: Scout without overlay, adapt scale for each graph when "Uniformize" option is unchecked (mixing sources + zscores)
 * Waitbars:
  * Replace old waitbars with java ones
  * Add a "Cancel" button on waitbars when the bounds are defined (ie. when bst controls the process)
 * Double-click doesn't work well on some Linux workstations
 * Bug: Menu "Use default EEG cap" doesn't work for a multiple selection (setting the same EEG cap for several subjects)
 * Bug node selection: click on sources > TF: select node-source, not node-condition
 * Bug 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
+ * Use Matlab Coder to optimize some processes: Bandpass filter, sinusoid removal
 * Hide Java panels instead of deleting them
 * mri2scs: convert arguments to meters
-Line 222:
+Line 210:
- * Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)...
 * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
-Line 225:
+Line 211:
- * Write shepards.m with new algorithm for nearest neighbors
 * Use Matlab Coder to compile / optimize some processes
 * Optimize calls to bst_get, now study and subject have necessarily the same folder name
+ * 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
 * Line smoothing / anti-aliasing (time series figures)
 * Optimize reload time

Software

Users

Development

What's next

Current topics

Functionnal connectivity

EEG / epilepsy / intra-cranial recordings

Source modeling

Large scale analysis

Recordings

Connectivity

Processes

Database

Source modeling

Anatomy

Statistics

Input / output

Distribution & documentation

Current bugs

Geeky programming details