Differences between revisions 13 and 126 (spanning 113 versions)

What's next

A roadmap to the future developments of Brainstorm.

Current topics

Functionnal connectivity

Significance thresholding of the connectivity matrices

Documentation

Merging the 12+3 introduction tutorials to illustrate better the latest developments

Source modeling

Implementation of a new unified minimum norm/beamformer framework

Compatibility

Reading and writing FieldTrip structures
Calling FieldTrip functions from the pipeline editor

Recordings

Nicer 2D topographies, standardized
RAW file viewer:
- Pre-load next page of recordings
- Documentation: Add definition of bad segments
- 2DLayout: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
EEG reference/storage:
- Intracranial electrodes: Define in the MRI viewer
- 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
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
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
Copy figures to clipboard (with the screencapture function)

Connectivity

Tutorial coherence [1xN]
Thresholding the connectivity matrices
t-tests on connectivity measures
Graph view:
- Fixed scales for intensity sliders
- Fix zoom in one region
- Text bigger
- Too much data in appdata
Other metrics:
- Coherence by bands: bst_coherence_band_welch.m
- Granger by bands: bst_granger_band.m
- Inter-trial coherence
Work on progress bars

Processes

Distributed processing: Brainstorm that can run without Java
Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
Allow processes in Python and Java
SSP:
- Make average the default option
- 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:
- Rewrite without the force low-pass filter at Fs/3
- Show warning when using inappropriate high-pass filter (precision too high)
- Use FIR filter
ICA for cleaning eye movements in EEG low density (SSP don't work well)
Reports:
- Save as HTML / PDF
- Do not display the intermediate files
Pipeline editor:
- Add loops over subjects/conditions/trial groups
Time-frequency:
- Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
- 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 ?)
- TF scouts: should display average of TF maps
Artifact detection:
- Detection of bad segments in the RAW files (Beth)
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
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:
- 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)

Database

Optimize startup speed
Start Brainstorm without Java (-nodesktop)
Sort files by comment
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
Rename multiple files
Allow matrix files to be attached to other files

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
PSOM: http://psom.simexp-lab.org/

Source modeling

Finish dipole scanning (allow the tab to control multiple figures separately)
Dipole fitting
Panel Get coordinates: Add button "find maximum"
Stenroos 2014 paper: Include the following methods
- Inner and outer skull surfaces generator from FieldTrip (needs SPM, probably not so different from BST)
- 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:
- 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:
- 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
- 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?
Processes compute head model and sources: Additional option to set the file comment
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
bst_wmne: Dirty patch with schur() to redo the decompositions where eig return complex values. Should be done in a cleaner way

Anatomy

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
- 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?
Smooth surface: Fix little spikes to irregularities in the mesh
Menu head model > Copy to other conditions/subjects (check if applicable first)

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
  - 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
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
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

Input / output

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_*)
EEG File formats:
- EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
BCI2000 Input (via EEGLAB plugin)
EEGLAB import:
- Selection of conditions in script mode
- Support for binary AND epoched files (now it's one or the other)
- Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
BST-BIN: Add compression

Distribution & documentation

Rewrite basic 12+3 tutorials: group in one series
- Illustrate 2D Layout
- Illustrate unconstrained sources
Cleaning threads on the forum
Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
Publication list: Fold by years
Finish existing tutorials:
- Dipoles
- Auditory: Extend to MNE/EEGLAB/SPM
- Auditory: Finish scripts
- Group MEM/Epilepsy + Epilepsy tutorials
New tutorials:
- MEG connectome
- Scrambled faces (SPM/MNE-Python)
- Describe all the processes
- Statistics
- Coherence (cortico-muscular ?)
- Intra-cranial recordings (Average ref by groups using Comment field)
- Co-register MEG runs (Beth)
Missing in the introduction tutorials:
- Volume scouts
- 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)
- Time-frequency: Description of "log freq scale" option
Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
Missing in page "Cite Brainstorm": Add all the methods used in the software
Reference tutorials on Google scholar
Play videos on wiki with <video> tag (save videos in .ogg)

Current bugs

Workshops:
- Create scouts doesn't work: scout created on the other side of the brain
- Import anatomy folder: Out of memory sometimes (restart Matlab)
- 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"
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
2DLayout (TF): Images are too far apart with EEG 20 channels

Geeky programming details

Removing all the CTRL and SHIFT in the keyboard shortcuts
Hide Java panels instead of deleting them
mri2scs: convert arguments to meters
Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b)
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)
Fix all the 'todo' blocks in the code
Replace handle "0" with bst_get('groot')
At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
Error message: Add a link to report directly the bug on the forum
in_bst_results (isFull=1): DataFile should be relative

-  ⇤ ← Revision 13 as of 2011-12-13 15:22:24 → 
  Size: 11587
  Editor: grumio
  Comment:
+   ← Revision 126 as of 2014-11-14 23:42:02 → ⇥
  Size: 15397
  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 ==
==== 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
+A roadmap to the future developments of Brainstorm.

== Current topics ==
-Line 20:
+Line 6:
- * Implementation of methods developed at USC

<<BR>><<BR>>

== Details of those features ==
+ * Significance thresholding of the connectivity matrices

==== Documentation ====
 * Merging the 12+3 introduction tutorials to illustrate better the latest developments

==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework

'''Compatibility'''

 * Reading and writing !FieldTrip structures
 * Calling !FieldTrip functions from the pipeline editor

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

== Recordings ==
 * Nicer 2D topographies, standardized
 * RAW file viewer:
  * Pre-load next page of recordings
  * Documentation: Add definition of bad segments
  * 2DLayout: Doesn't work when changing page => need refresh of !GlobalData.Preferences.!TopoLayoutOptions.!TimeWindow
 * EEG reference/storage:
  * Intracranial electrodes: Define in the MRI viewer
  * 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
 * 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
 * Filtering: Use short FIR filters instead of IIR for bandpass, to limit the ringing<<BR>>Or allow the users to edit the !LowStop parameter in bst_bandpass.

 * Show easily recordings maximum/values in the file viewer
 * Copy figures to clipboard (with the screencapture function)

== Connectivity ==
 * Tutorial coherence [1xN]
 * Thresholding the connectivity matrices
 * t-tests on connectivity measures
 * Graph view:
  * Fixed scales for intensity sliders
  * Fix zoom in one region
  * Text bigger
  * Too much data in appdata
 * Other metrics:
  * Coherence by bands: bst_coherence_band_welch.m
  * Granger by bands: bst_granger_band.m
  * Inter-trial coherence
 * Work on progress bars

== Processes ==
 * Distributed processing: Brainstorm that can run without Java
 * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
-Line 26:
+Line 66:
-  * 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
 * RAW file viewer:
  * Buttons for changing scales (time + amplitude)
  * Add tooltips to all the buttons / shortcuts
  * Adding events using configurable shortcuts (CTRL+number)
  * If "Use SSP " option is selected, automatically select "Remove baseline" and "CTF compensations"
  * Documentation: Add definition of bad segments
 * RAW processing:
  * 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)
 * 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
 * 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
 * Visualize Beamformer results (contact Zainab Fatima):
  * Read CTF SAM .svl
  * Create new file type in the database
  * Display as layers in the MRI viewer
 * ICBM brain
  * MINC MRI reader: EMMA, NIAK (Pierre Bellec), HDF5 directly read in Matlab
  * ICBM average surfaces + atlas
  * Using CIVET pipeline for extracting surfaces

== Other new features ==
 * Intracranial electrodes:
  * Display in the MRI viewer
  * Different data type
  * Display time series
 * Stat on scouts / clusters / "matrix"
+  * Make average the default option
  * Display warning if changing the !ChannelFlag while there is a Projector applied
  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * Bandpass:
  * Rewrite without the force low-pass filter at Fs/3
  * Show warning when using inappropriate high-pass filter (precision too high)
  * Use FIR filter
 * ICA for cleaning eye movements in EEG low density (SSP don't work well)
 * Reports:
  * Save as HTML / PDF
  * Do not display the intermediate files
 * Pipeline editor:
  * Add loops over subjects/conditions/trial groups
 * Time-frequency:
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * 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 ?)
  * TF scouts: should display average of TF maps
 * Artifact detection:
  * Detection of bad segments in the RAW files (Beth)
  * Artifact rejection like SPM: if bad in 20%, bad everywhere
  * Test difference between adjacent samples
-Line 73:
+Line 92:
-  * By subject AND condition
 * Command-line Brainstorm: for working on clusters (make sure that there are no interface interruptions)
 * GUI: Save configuration of windows (per protocol)
+  * 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:<<BR>>
  * 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)

== Database ==
 * Optimize startup speed
 * Start Brainstorm without Java (-nodesktop)
 * Sort files by comment
-Line 78:
+Line 116:
- * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * 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)
+ * Group matrix files => allow to process matrix files by trial types
-Line 85:
+Line 120:
+ * Screen captures: save straight to the database

 * Rename multiple files

 * Allow matrix files to be attached to other files

== 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
 * PSOM: http://psom.simexp-lab.org/
-Line 86:
+Line 136:
+ * Finish dipole scanning (allow the tab to control multiple figures separately)
 * Dipole fitting
 * Panel Get coordinates: Add button "find maximum"
 * Stenroos 2014 paper: Include the following methods
  * Inner and outer skull surfaces generator from !FieldTrip (needs SPM, probably not so different from BST)
  * 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
-Line 88:
+Line 148:
-  * Define as default
  * Check all the processes
-Line 91:
+Line 149:
+  * Stat and connectivity: what to do? (re-send email John+Sylvain)
-Line 97:
+Line 156:
-  * Optimize: grid_interp_mri
 * Magnetic extrapolation:
  * Do the same thing with EEG
  * 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
+ * Magnetic extrapolation: Do the same thing with EEG
-Line 107:
+Line 158:
+  * 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?
-Line 109:
+Line 164:
+ * 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?
 * Processes compute head model and sources: Additional option to set the file comment
 * 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
 * bst_wmne: Dirty patch with schur() to redo the decompositions where eig return complex values. Should be done in a cleaner way
-Line 111:
+Line 176:
- * BEM:
  * Fix the bumps at the back of the head
  * Surface edges: same color as the surface when color was changed
 * Improve ICP registration headpoints / scalp (chanfrein, multi-resolution, see with C Grova...)
 * Use BrainVISA / FreeSurfer labeling automatically when importing cortex surfaces
 * 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 ==
 * Other processes:
  * Moving average
  * Remove linear trend
  * Power line removal
  * 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:
  * 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
+ * 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
  * 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?
 * Smooth surface: Fix little spikes to irregularities in the mesh
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
-Line 151:
+Line 196:
+   * 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
-Line 157:
+Line 205:
-== 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
 * 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

== Input / output ==
 * 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_*)
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+Line 221:
-  * Stellate
  * !BrainVision / !BrainAmp: Get functions from EEGLAB
  * Nihon Kohden
  * EDF+
-Line 175:
+Line 222:
-  * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler
-Line 177:
+Line 223:
- * 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
  * Gzipped Nifti (new BrainVISA standard)
  * Output for all the channel file formats
  * 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
+ * BCI2000 Input (via EEGLAB plugin)
 * EEGLAB import:
  * Selection of conditions in script mode
  * Support for binary AND epoched files (now it's one or the other)
  * Allow epoched files with recordings saved in external files (now external files implies continuous recordings)
 * BST-BIN: Add compression

== Distribution & documentation ==
 * Rewrite basic 12+3 tutorials: group in one series
  * Illustrate 2D Layout
  * Illustrate unconstrained sources
 * Cleaning threads on the forum
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.

 * Publication list: Fold by years
 * Finish existing tutorials:
  * Dipoles
  * Auditory: Extend to MNE/EEGLAB/SPM
  * Auditory: Finish scripts
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG connectome
  * Scrambled faces (SPM/MNE-Python)
  * Describe all the processes
  * Statistics
  * Coherence (cortico-muscular ?)
  * Intra-cranial recordings (Average ref by groups using Comment field)
  * Co-register MEG runs (Beth)
 * Missing in the introduction tutorials:
  * Volume scouts
  * 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)
  * Time-frequency: Description of "log freq scale" option
 * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
 * Missing in page "Cite Brainstorm": Add all the methods used in the software
 * Reference tutorials on Google scholar
 * Play videos on wiki with <video> tag (save videos in .ogg)

== Current bugs ==
 * Workshops:
  * Create scouts doesn't work: scout created on the other side of the brain
  * Import anatomy folder: Out of memory sometimes (restart Matlab)
  * 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"
 * 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
 * 2DLayout (TF): Images are too far apart with EEG 20 channels
-Line 191:
+Line 289:
- * 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
+ * Removing all the CTRL and SHIFT in the keyboard shortcuts
 * Hide Java panels instead of deleting them
 * mri2scs: convert arguments to meters
 * Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (Matlab 2014b)
-Line 196:
+Line 294:
- * 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)...
 * sLORETA: Values are now multiplied by 1e12 at loading for display => has do to be done in another way
-Line 200:
+Line 295:
- * 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

== Distribution & documentation ==
 * Version with big fonts for live demos
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
 * List of all the shortcuts
 * 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
 * Introduction tutorials:
  * Estimate time to complete each tutorial
  * Clusters
  * Anatomy: Segmentation with !FreeSurfer
  * First steps: Brainstorm preferences
  * Headmodel: explain the fields + how to get the constrained leadfield
  * Coordinate sytems: How to convert between the different coordinates systems in scripts
  * Sources: Modelized data
  * Sources: theshold min. size (not documented yet)
  * 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
  * Import raw recordings: Add "detect bad trials/channels" in the pipeline
 * Advanced tutorials:
  * MNE sample dataset
  * EEG (How to import an EEG cap)
  * 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
+ * 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)
 * Fix all the 'todo' blocks in the code
 * Replace handle "0" with bst_get('groot')
 * At the end of bst_startup in compiled mode, replace loop with waitfor(jFrame)
 * Error message: Add a link to report directly the bug on the forum
 * in_bst_results (isFull=1): DataFile should be relative

Software

Users

Development

What's next

Current topics

Functionnal connectivity

Documentation

Source modeling

Recordings

Connectivity

Processes

Database

Distributed computing

Source modeling

Anatomy

Statistics

Input / output

Distribution & documentation

Current bugs

Geeky programming details