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| A to-do list for the development of Brainstorm in the next few years == New interface elements == |
A roadmap to the future developments of Brainstorm. == Current topics == ==== Functionnal connectivity ==== * 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 * 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:<<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? == 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 * Detection of bad segments in the RAW files * 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:<<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 == |
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| * Functionnal connectivity (display: see eConnectome) * SSP: * 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 * 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 * 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 |
* Add notes in the folders (text files, visible as nodes in the tree) * Screen captures: save straight to the database |
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| * 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 |
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| * Define as default * Check all the processes |
* Compute unconstrained and then project on the normal ? |
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| * Stat and connectivity: what to do? (re-send email John+Sylvain) | |
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| * Optimize: grid_interp_mri | |
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| * 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 |
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| * 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? |
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| * 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 |
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| * 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 * 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? |
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== 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. == Input / output == |
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| * Nihon Kohden * EDF+ * !BrainVision / !BrainAmp: Get functions from EEGLAB |
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| * NEUROFILE = COHERENCE EEG/video !LongTerm Monitoring => Manfred Spueler | |
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| * 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) |
* !FieldTrip structures: In / Out * BCI2000 Input (via EEGLAB plugin) * Export TF maps to SPM / volumes |
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| * Compile stand-alone version: Linux, MacOS * Version with big fonts for live demos |
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| * 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 |
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| * Estimate time to complete each tutorial | * Processes: Describe all the processes |
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| * Anatomy: Segmentation with !FreeSurfer | |
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| * Coordinate sytems: How to convert between the different coordinates systems in scripts | |
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| * 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 |
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| * Temporary folder | |
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| * MNE sample dataset | |
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| * 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 |
* 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 |
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
- Detection of bad segments in the RAW files
- 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.
- 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
- 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
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.
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
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