Differences between revisions 5 and 89 (spanning 84 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
- 2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
EEG reference/storage:
- Intracranial electrodes: Define and display in the MRI viewer + 3D figures
- Re-reference recordings
- 2D topo plots: Display bipolar montages with electrodes positions = average of the two electrodes
- Bad locations: indicate with [NaN NaN NaN] instead of [0 0 0]
- Location of bipolar electrodes: Save the 2 positions in the channel file, with weights=[1 -1]
- Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
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
Colormaps:
- Create a colormap similar to MNE, where extrema are bright
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
Bandpass: Show warning when using inappropriate high-pass filter (precision too high)
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
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?

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)

Current bugs

Record tab: Text of epoch number is too big on MacOS
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
Problems growing scouts on merged surfaces (Emily)

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)

-  ⇤ ← Revision 5 as of 2011-12-12 22:47:33 → 
  Size: 11412
  Editor: grumio
  Comment:
+   ← Revision 89 as of 2014-01-22 17:07:29 → ⇥
  Size: 11069
  Editor: agrippa
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-A roadmap for the future developments of Brainstorm.

== Next six months ==
==== Continuous recordings in native format ====
 * Extend processing of continuous CTF files to all file formats
 * Improve detection and correction of artifacts with SSP
 * Continuous viewer: Many small improvements to the usability of its interface
+A roadmap to the future developments of Brainstorm.

== Current topics ==
-Line 11:
+Line 6:
- * Implementation of methods developed at USC

<<BR>><<BR>>

== New interface elements ==
+ * 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

<<BR>><<BR>><<BR>>

== 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
  * 2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
 * EEG reference/storage:<<BR>>
  * Intracranial electrodes: Define and display in the MRI viewer + 3D figures
  * Re-reference recordings
  * 2D topo plots: Display bipolar montages with electrodes positions = average of the two electrodes
  * Bad locations: indicate with [NaN NaN NaN] instead of [0 0 0]
  * Location of bipolar electrodes: Save the 2 positions in the channel file, with weights=[1 -1]
  * Bad channels that can be specified at the program level (for sites that have permanently bad channels) => AS Dubarry
 * 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
 * Colormaps: <<BR>>
  * Create a colormap similar to MNE, where extrema are bright
 * 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
 * Bandpass: Show warning when using inappropriate high-pass filter (precision too high)
 * 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 17:
+Line 83:
-  * Write documentation
  * 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
 * RAW file
 * 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
+  * 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)
 * 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<<BR>>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 ==
-Line 27:
+Line 110:
- * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * 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)
 * Images of amplitude: [sensor x time], [trial x time], scout: [trial x time] (similaire to erpimage in eeglab)
 * Simulation: synthesize pseudo data-files from a cortex patch (duration, amplitude, noise)
 * Interface to compute reaction times based on events: <<BR>>Input:selection  of cue event + event response; Output: reation time trial by trial,  average, std, distribution... => Etienne Labyt
 * Database navigator: F4 to switch to next sourcefile
 * Segmentation in microstates
+ * 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
-Line 39:
+Line 117:
- * Inverse:
  * Stable LCMV Beamformer
  * MUSIC
  * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
+ * 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
-Line 44:
+Line 123:
-  * Define as default
  * Check all the processes
+  * Compute unconstrained and then project on the normal ?
-Line 47:
+Line 125:
+  * Stat and connectivity: what to do? (re-send email John+Sylvain)
-Line 53:
+Line 132:
-  * Optimize: grid_interp_mri
-Line 56:
+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 63:
+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 65:
+Line 140:
+ * 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
 * 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?
-Line 67:
+Line 147:
- * MRI import: auto-reorientation of MRI  after selected NAS / LPA / RPA.
 * Major bug when importing surfaces for an MRI that was re-oriented manually
 * Finalize Brodmann scouts
 * Remove NCS/Talairach coordinate system, or fix it => Sylvain, Karim ND
 * Clustering cortex: Dimitrios, David, Yu-Teng

== Processes ==
 * Important new processes for a full processing pipleline:
  * Import, and segmentation of RAW files
  * Detect bad segments on RAW (then events in "bad" segments would be ignored)
  * Artifact detection: use other things than simple value thresholds (like variance of the sensors...)
  * Create events list based on thresholds on some channels (Stim, EOG, ECG...) => Etienne Labyt
  * Creation of SSP vectors (ex: Remove cardiac artifac)
  * ICA
  * Integration of Antoine Ducorps methods (everything in the doc of the dataHandler):
   * Cardiac artifact correction in MEG
   * PCA correction of ocular artifacts
   * Interpolation of missing EEG canal
  * Headmodel / sources / noise cov
  * Project sources
  * Delete intermediary files
 * Processing raw/continuous:
  * Process non-FIF files (need to convert the header)
  * Apply SSP + CTF Compensators(only if it useful - maybe create a specific process for that)
 * Other processes:
  * Bug: gradnorm crashes with bad channels
  * Spatial smoothing: check / document parameters
  * Sinusoid removal: fix new function
 * 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:
  * 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
 * John's noise cancellation filters
 * Chain calls of similar processes (ex. bandpass+sin_remove), to avoid reading the full raw files several times
+ * 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?
-Line 122:
+Line 171:
-== Display ==
 * OpenGL options: {none, software, hardware}
 * Colormap: Set colormap max with right-click + move on the colorbar
 * Bug: Mixing 2 views MRI/3d, white cuts appear after !SetCurrentFigure
 * 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)
 * Contact sheets & movies: use average of time windows instead of single instants, for each picture.

== I/O ==
+ * t-test on volume sources
 * Create icons for Stat/PAC, Stat/Sprectrum, etc.
 * One sample t-test across subjects

== Input / output ==
-Line 135:
+Line 177:
-  * Nihon Kohden
  * EDF+
  * !BrainVision / !BrainAmp: Get functions from EEGLAB
-Line 139:
+Line 178:
-  * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler
-Line 141:
+Line 179:
- * Other file formats
  * MEG160  (KIT)
  * CTF:
   * Read continuous RAW files split in several .meg4 files ( > 2 Go)
   * Read STIM channel and generate !MarkerFile
  * EEGLAB: Apply ICA matrices, get number of trials for AVG files
  * !FieldTrip structures: In / Out
  * Gzipped Nifti (new BrainVISA standard)
  * Analyze / Nifti:<<BR>>
   * Fix output function (output MRIs cannot be  imported in SPM)
   * Use correctly field "orient" to align automatically MRI when importing
 * Define scouts from SPM / Analyze 3D masks
 * Files > 2Gb: display warnings

== Programming details ==
 * 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
 * bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
 * Testing functions: test_ctf "folder" / test_neuromag "folder" / test "folder" => Alex
 * Bug in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)...
 * Shared kernels: do the "get bad channels" operation in a different way (reading all the files is too slow)
 * Rewrite all GUI functions with gui_component
 * Remove field "!BrainStormSubject" in the studies file: force same folder name for anat & data
 * Allow protocols with same folder for anat and data
 * Ensure that all the loaded and saved filenames are in "unix" format
 * Use parfor: When not available, replace directly all the "parfor" with "for" in file.m
 * Use Matlab GPU toolbox
 * Re-use panels instead of delete+create again
 * Optimize bst_read_events_track
 * Write shepards.m with new algorithm for nearest neighbors
 * Use tesselations_stat and tesselations_outwards to clean surfaces
 * Movies: Use JAVE (Java)
 * Screen captures: Use Yair Altman functions (in Matlab Central)
 * Use Matlab Coder to compile / optimize some processes
+ * !FieldTrip structures: In / Out
 * BCI2000 Input (via EEGLAB plugin)
 * Export TF maps to SPM / volumes
 * EEGLAB import: Selection of conditions in script mode
-Line 179:
+Line 185:
- * Compile stand-alone version: Linux, MacOS
 * Version with big fonts for live demos
-Line 182:
+Line 186:
- * Send email to registered users to anounce major improvements
 * Script tutorials:
  * Update them to reflect all the recent changes
  * Script for the time-frequency computation
 Line 187:
-  * Estimate time to complete each tutorial
+  * Processes: Describe all the processes
 Line 189:
-  * Anatomy: Segmentation with !FreeSurfer
-Line 192:
+Line 191:
-  * Coordinate sytems: How to convert between the different coordinates systems in scripts
-Line 195:
+Line 193:
-  * 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 200:
+Line 194:
+  * Temporary folder
-Line 201:
+Line 196:
-  * MNE sample dataset
-Line 203:
+Line 197:
-  * 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

== Unsolved problems ==
 * Surfaces:
  * Influence of the software used to extract surfaces (!BrainVisa, !BrainSuite, !FreeSurfer)
  * Type  of cortex surface to use: grey/white, grey/csf, midsurface ?
  * How  to get good surfaces for BEM ?
 * Group analysis:
  * 1)  localization on individual brain + interpolation on MNI brain ?
  * 2)  localization directly on MNI brain ?
  * Normalize amplitudes  across different subjects / runs ?
 * Online  documentation of forward and inverse methods
+== Current bugs ==
 * Record tab: Text of epoch number is too big on MacOS
 * 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
 * Problems growing scouts on merged surfaces (Emily)

== 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)

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