Differences between revisions 204 and 467 (spanning 263 versions)

What's next

A roadmap to the future developments of Brainstorm.

Contents

Recordings
Interface
Connectivity
Processes
Database
Distributed computing
Source modeling
Anatomy
ECOG/SEEG
Statistics
Input / output
Distribution & documentation
Current bugs
Geeky programming details

Recordings

Sleep scoring wish list (Emily C):
- Configurable horizontal lines (for helping detecting visually some thresholds)
- Mouse ruler: Measure duration and amplitude by dragging the mouse.
- Automatic spindle detector
- https://neuroimage.usc.edu/forums/t/page-overlap-while-reviewing-raw-file-a-way-to-set-to-0/11229/13
RAW file viewer:
- Downsample before filtering? (attention to the filter design)
- Add parameter to make the visual downsampling more or less aggressive
- Pre-load next page of recordings
- Keep the filter specifications in memory instead of recomputing for every page
Bad trials: When changing the status of bad to good: remove the bad segments as well, otherwise it is not processed by processes like the PSD.
Review clinical recordings: Reduce the dimensionality of the data with a simple inverse problem, similar to what we do for the magnetic extrapolation ("Regional sources" in BESA, cf S Rampp)
MEG/EEG registration: Apply the same transformation to multiple runs
Create heat maps: Maybe with matlab function heatmap?
BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)

Interface

Add a warning when computing a forward model with > 100000 sources (check selection)
Snapshot: Save as image / all figures (similar to Movie/all figure)
Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly
Colormaps:
- Allow brightness/contrast manipulations on the custom colormaps
- Global colormap max: Should get the maximum across all the open files
Copy figures to clipboard (with the screencapture function)
Smooth display from figure_image (ERPimage, raster plot...)
Contact sheets & movies: use average of time windows instead of single instants, for each picture.
Contact sheets: Allow explicit list of times in input (+ display as in MNE-Python with TS)
Display CTF coils: Show discs instead of squares
Use boundary() instead of conhull() in all the display functions (ie. 2DDisc)
Progress bar: Add a "Cancel" button
Error message: Add a link to report directly the bug on the forum
Reorganize menus (Dannie's suggestion):

Connectivity

Thresholding and stat tests the connectivity matrices
Connectivity on unconstrained sources: "Default signal extraction for volume grids should be the time series of the first principal component of the triplet signals after each has been zero-meaned" (SB)
Display of connectivity graphs:
- Display as straight lines
- Recode 2D graphs
- 3D display with anatomical constrains
- Display using real position of EEG electrodes
Use new band-pass filters in bst_connectivity ('bst-hfilter' instead of 'bst-fft-fir')
Matrix view of NxN graphs: Add legend of the elements along X and Y axis
Weighted Phase Lag Index (WPLI)
Graph view:
- Does not display negative values correctly (correlation or difference of coherence)
- Re-write using pure Matlab code and smoothed graphics
- Fixed scales for intensity sliders
- Text bigger
- Too much data in appdata
- Fixed scales for intensity sliders
- Add "=" shortcut for having graphs with similar configurations
- Disable zoom in one region (serious bugs)
- NxN on sensors: does not place the sensors correctly in space
Coherence:
- Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
  Explore inter-trial approaches (Esther refers to chronux toolbox)
Granger: Check for minimum time window (Esther: min around 500-1000 data points)
PLV:
- Add p-values
- Remove evoked
- Optimize code
- Add time integration
- Unconstrained sources
- Add warning when running of short windows (because of filters)
Time-resolved correlation/coherence: Display as time bands
Tutorial coherence [1xN] : Reproduce FieldTrip results?
Connect NxN: Display as time series > Display warning before trying to open too many signals

Processes

Decoding/Classifiers: Implement Dimitrios and scikit-learn algorithms
Allow processes in Python and Java
Add MNE-Python functions:
- scikit-learn classifiers
- Implement data exchange with MNE-Python: write FIF files from Brainstorm and/or pass python objects in memory instead of FIF files
- https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3
- SSS/tSSS cleaning
- Reproduce other tutorials / examples
- Change the graphic renderer from Matlab
Add FieldTrip functions:
- ft_sourceanalysis:
  - Check noise covariance
  - Check all the options of all the methods
  - Single trial reconstructions + noise covariance?
  - Filters?? http://www.fieldtriptoolbox.org/example/common_filters_in_beamforming
  - Beamformers: Save ftSource.avg.mom
    http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo
  - http://www.natmeg.se/ft_beamformer/beamformer.html
  - http://www.fieldtriptoolbox.org/tutorial/beamformingextended
  - Baseline? Two inputs?
- ft_prepare_sourcemodel: Compute MNI transformation (linear and non-linear) => Peter
- ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database
- Freqanalysis: ITC
- ft_read_atlas('TTatlas+tlrc.BRICK');
- ft_volumereslice: http://www.fieldtriptoolbox.org/faq/how_change_mri_orientation_size_fov
- ft_freqanalysis
- ft_combineplanar
Optimization:
- Use CUDA for speeding up some operations (filtering, wavelets, etc)
- Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
Pipeline editor:
- Bug: After "convert to continuous", the time of the following processes should change
- Add loops over subjects/conditions/trial groups
- Events: Allow selection from a drop-down list (similar to option "channelname" in panel_process_selection)
- When computing sources from the pipeline editor: doesn't reselect the options if you click twice on "edit" (works for minnorm, but not for lcmv)
ITC: Inter-trial coherence (see MNE reports for group tutorial)
http://www.sciencedirect.com/science/article/pii/S1053811916304232
ICA:
- Why doesn't the ICA process converge when using 25 components in the EEG tutorial?
- Add an option to resample the signals before computing the ICA decomposition
- Exploration: Add window with spectral decomposition (useful for muscle artifacts)
- Export IC time series (and then compute their spectrum): solves the problem above
- Comparison JADE/Infomax:
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030135
- Use faster methods (MNE-Python?)
- Add methods: SOBI, Fastica, AMICA/CUDICA (recommended by S Makeig)
- Dimension reduction with PCA adds artifacts: Not done by default in EEGLAB
  Contact: Stephen Shall Jones ( shall-jones@infoscience.otago.ac.nz )
  Student Carl Leichter detailed this in his thesis
- S Makeig: Use ICA to select the IC of interest instead of only removing artifacts
- Display of spectrum for components (PSD/FFT)
- Import ICA matrices available in EEGLAB .set files
- EEGLAB recommends ICA + trial rejection + ICA again: Impossible right now with Brainstorm
  (http://sccn.ucsd.edu/wiki/Chapter_09:_Decomposing_Data_Using_ICA)
- ICA+machine learning: https://www.ncbi.nlm.nih.gov/pubmed/28497769
- Automated artifact rejection: https://arxiv.org/abs/1612.08194
- Use EYE-EEG: EEGLAB toolbox for eye-tracker guided ICA (Olaf Dimigen): http://www2.hu-berlin.de/eyetracking-eeg/
Other EEGLAB functions:
- Step function detection: https://github.com/lucklab/erplab/wiki/Artifact-Detection:-Tutorial
SSP:
- Display warning if changing the ChannelFlag while there is a Projector applied
Spectral flattening (John):
- ARIMA(5,0,1): Apply on the signal before any frequency/connectivity/PAC analysis
PSD:
- Rewrite to have the same input as coherence (frequency resolution instead of window length)
- Allow display of Avg+StdErr
Remove line noise: http://www.nitrc.org/projects/cleanline
Time-frequency:
- Optimization: bst_timefreq (around l.136), remove evoked in source space: Average should be computed in sensor space instead of source space (requested by Dimitrios)
- Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
- Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
- Bug: Display logs as negative
- Bug: 3D figures: Colormaps with "log" option doesn't work
- Bug: Difference of power displayed in log: problems (Soheila)
- 2D Layout in spectrum
- Make much faster and more memory efficient (C functions coded by Matti ?)
- TF scouts: should display average of TF maps
- Impossible to keep complex values for unconstrained sources
- Pad short epochs with zero values for getting lower frequencies
- Hilbert with time bands very slow on very long files (eg. 3600s at 1000Hz) because the time vector is still full (10^7 values): save compressed time vector instead.
- Extend clusters tab to display of TF to overlay TF signals (Svet)
- When normalizing with baseline: Propagate with the edge effects marked in TFmask
- Allow baseline normalization of files computed with time bands
- Allow running TF on montages
- Review continuous files in time-frequency space (for epilepsy)
- Bug when computing TF on constrained and unconstrained scouts at the same time (in mixed head models for instance): uses only the constrained information and doesn't sum the 3 orientations for the unconstrained regions.
Artifact detection:
- Artifact rejection like SPM: if bad in 20%, bad everywhere
- Test difference between adjacent samples
Events detection: Add option "std" vs "amplitude"
Simulation:
- EEGSourceSim: https://www.sciencedirect.com/science/article/pii/S0165027019302341
- Fix units in simulation processes => no *1e-9 in "simulate recordings"
- Use "add noise" process from Hui-Ling (in Work/Dev/Divers)
Use field process field "Group" to separate Input/Processing/Output options
Use new Matlab functions: movmean, movsum, movmedian, movmax, movmin, movvar, movstd

Database

MEG protocols: More flexible organization of the database; sub-conditions to allow different runs X different conditions.
Matrix files: Allow to be dependent from other files
Rename multiple files
Default headmodel lost when reloaded: Keep selection on the hard drive (in brainstormstudy.mat)
Auto-save:
- protocol.mat can be too big: do not store the results links in it (and recreate when loading)- http://neuroimage.usc.edu/forums/t/abnormally-slow-behavior/2065/10
- Improve auto-save: add tracking file next to protocol.mat, do not save all the time, only when closing app, and reload protocol at stratup if tracking file is still there

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/
Various initiatives: http://samirdas.github.io/Data_sharing.html#/

Source modeling

Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
Reproduce results in "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
Use eLORETA instead of sLORETA?
https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
- "eLORETA algorithm is available in the MEG/EEG Toolbox of Hamburg (METH)": https://www.biorxiv.org/content/biorxiv/early/2019/10/17/809285.full.pdf
Point-spread and cross-talk functions (code in MNE-Python):
- https://www.biorxiv.org/content/biorxiv/early/2019/06/18/672956.full.pdf
- https://github.com/olafhauk/EEGMEGResolutionAtlas
Dipoles:
- Project individual dipoles files on a template
- panel_dipoles: Doesn't work with multiple figures
Project sources: Very poor algorithm to project sub-cortical regions and cerebellum (algorithm to fit surfaces should be imrpoved)
Menu head model > Copy to other conditions/subjects (check if applicable first)
Menu Sources > Maximum value: Doesn't work with volume or mixed head models
Mixed head models:
- Set loose parameter from the interface
- Bug when displaying interpolated in MRI viewer
Volume grid:
- Optimize: 3D display (better than 9x9 cubes)
- Optimize: vol_dilate (with 26 neighbors)
Menu Sources > Simulate recordings:
- Do not close the 3D figures after generating a new file
- Add a process equivalent to this menu
Panel Get coordinates: Add button "find maximum"
BEM single sphere: Get implementation from MNE
Unconstrained sources:
- Stat and connectivity: what to do? (re-send email John+Sylvain)
Sources on surface: Display peak regions over time (time = color) => A.Gramfort
Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
Add eyes models to attract eye activity
Display source maps on a flat 2D cortex projection (Mollweide projection): https://neuroimage.usc.edu/forums/t/source-model-display-and-output/13940/5

Anatomy

CAT12: Optimize interpolation of atlases (import is super slow...)
SimNIBS: Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)
Keep ASEG volume + display region name in MRI viewer
Multi-Scale Brain Parcellator (Lausanne2008):
MNI transformation: Use SPM non-linear MNI transformation y_...
Registration:
- Getting electrode positions from 3D scanners: https://sccn.ucsd.edu/wiki/Get_chanlocs
- GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
- Use the same registration for multiple recording sessions that have already re-registered previously (eg. with MaxFilter)
- When linking multiple EEG recordings including 3D positions, do the registration only once and copy it to all the runs
- Compute non-linear MNI registration instead of linear
- Select and remove bad digitized head points before automatic coregistration
- Load the MNE -transf.fif: http://neuroimage.usc.edu/forums/showthread.php?2830
MRI Viewer:
- Pan in zoomed view (shift + click + move?)
- Zoom in/out with mouse (shift + scroll?)
- Ruler tool to measure distances
- Display scouts as additional volumes
- Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
  Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
- Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
- Optimize computation interpolation MRI-surface (tess_tri_interp) => spm_mesh_to_grid
BrainSuite:
- Add new labels to all BrainSuite anatomy templates
- Use same colors for left and right for anatomical atlases
- Use for volume coregistration (rigid / non-rigid)
FEM templates for different ages:
- Pediatric head atlases: https://www.pedeheadmod.net/pediatric-head-atlases-v1-2/
- https://iopscience.iop.org/article/10.1088/2057-1976/ab4c76
- https://www.biorxiv.org/content/biorxiv/early/2020/02/09/2020.02.07.939447.full.pdf
- John Richards: https://www.nitrc.org/frs/?group_id=1361
MRI to FEM mesh generation :
- Process the FEM cortex/source space (either from CAT or SimNibs) and fit all the dipoles within the grey matter (important in the case where white matter and scf are considered) to acheive the Venant condition (also for other source models
Scouts:
- Display edges in the middle of the faces instead of the vertices
- Display scouts in a tree: hemisphere, region, subregion
- Sort scouts by region in process options
- Downsample to atlas: allow on timefreq/connect files
- Project from one hemisphere to the other using registered spheres/squares (http://neuroimage.usc.edu/forums/t/how-to-create-mirror-roi-in-the-other-hemisphere/5910/8)
Parcellating volume grids: scikit-learn.cluster.Ward
Major bug when importing surfaces for an MRI that was re-oriented manually
Surface>Volume interpolation: Use spm_mesh_to_grid
Bug: Hide scouts in the preview of the grid for volume head models
Geodesic distance calculations:
https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching

ECOG/SEEG

Electrodes models: Import / export
Contact positions: Import / set / detect
- New option: Align on none|inner|cortex to replace ECOG-mid
- Add history: Save modifications and transformations applied to the channel files (Marcel)
- Project contact positions across subjects or templates (Marcel)
- Add menu to import implantation channel file in imported recordings
SEEG/ECOG: Identify contacts in resected areas / identify ROIs for each contact
SEEG/ECOG: Identify contacts in a give anatomical region (volume scout, surface mesh, or label in a volume atlas) / allow extracting the signals from all the contacts in an ROI
Automatic segmentation of CT:
ECOG:
- Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
- Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf
- ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage)
Display:
- Bad channels: Contacts greyed out instead of ignored (Marcel)
- Display time in H:M:S
- Display curved SEEG electrodes
Export list of contacts with a probability of anatomical regions from various atlases: https://neuroimage.usc.edu/forums/t/seeg-contacts-anatomical-location/14756
Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect

Statistics

ANOVA:
- Which functions to use?
- Write panel similar to Process1 and Process2 to allow the
- 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
Quality control before statistics, on condition averages across subjects:
mean(baseline)/std(baseline): shows bad subject quickly.
Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
Export to R or SPSS for advanced stat

Input / output

Bug import multiple files: use same "time" for all files
BIDS import:
- Read real fiducials
- Read associated empty room
- Test all the BIDS examples
BIDS Export:
- Add events ts, channel tsv, EEG, iEEG
XDF import: Use FieldTRip or the EEGLAB plugin, contact Martin Bleichner (Oldenburg)
https://github.com/sccn/xdf/blob/master/xdf_sample.xdf
DICOM converter:
- Add dcm2nii (MRICron)
- Add MRIConvert
FieldTrip: Import/Export time-frequency:
- Export: http://neuroimage.usc.edu/forums/t/export-time-frequency-to-fieldtrip/1968
- Import: http://neuroimage.usc.edu/forums/t/import-time-frequency-data-from-fieldtrip/2644
4D file format:
- Use reader from MNE-Python: mne.io.read_raw_kit (doesn't require Yokogawa slow library)
- Reference gradiometers: Keep the orientation of the first or second coil?
- Reference gradiometers: Add the sensor definition from coil_def.dat
- Validate with phantom recordings that noise compensation is properly taken into account
- The noise compensation is considered to be always applied on the recordings, not sure this assumption is always correct
- 4D phantom tutorial (JM Badier?)
EEG File formats:
- EEG CeeGraph
- EGI: Finish support for epoched files (formats 3,5,7)
- XLTEK: https://github.com/danielmhanover/OpenXLT
- Persyst .lay: https://github.com/ieeg-portal/Persyst-Reader
- Nervus .eeg: https://github.com/ieeg-portal/Nervus-Reader
- Biopac .acq: https://github.com/ieeg-portal/Biopac-Reader
- gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
BCI2000 Input (via EEGLAB plugin)
BST-BIN: Add compression to .bst
Review raw on all the file formats (ASCII EEG and Cartool missing)
SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
Get acquisition date from files: Missing for 4D
Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284

Distribution & documentation

Tutorial OMEGA/BIDS:
- Update the organization of derivatives folder (same for ECOG tutorial)
- Add review of literature for the resting state MEG
- Download example datasets directly from the OMEGA repository
New tutorials:
- Other public datasets: https://github.com/INCF/BIDS-examples/tree/bep008_meg/
- Rat PAC + high gamma (Soheila)
- EEG/research
- FieldTrip ECOG tutorial: http://www.fieldtriptoolbox.org/tutorial/human_ecog
- FieldTrip cortico-muscular coherence tutorial: http://www.fieldtriptoolbox.org/tutorial/coherence
- Reproduce tutorials from MNE-Python: https://martinos.org/mne/stable/tutorials.html
- Cam-CAN database: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/<<BR>>(download new datasets, including maxfiltered files and manual fiducial placements)
- MEG steady-state / high-gamma visual / frequency tagging
- BIDS-EEG example datasets
- Reproduce results from "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
Stand-alone ICA tutorial
Move all the files to download to the cloud for faster download everywhere in the world
Provide secure way of sending password over HTTPS for:
- Account creation
- Forum exchanges
- org.brainstorm.dialog.CloneControl
Workflows FieldTrip: http://www.fieldtriptoolbox.org/faq/what_types_of_datasets_and_their_respective_analyses_are_used_on_fieldtrip
Count GitHub clones in the the download stats
Deface the MRIs of all the tutorials
Clean up the wiki:
- Remove all the wiki pages that are not used
- Check all the links in all the pages
- Check that all the TODO blocks have been properly handled
- Remove useless images from all tutorials
- Update page count on the main tutorials page

Current bugs

MacOS 10.14.5 (Mojave):
- Toggle buttons do not show their status
- Panel Record: Text is too large for text boxes
Image viewer:
- Difficult to get to 100%
- Buggy on some systems
2DLayout:
- (TF) Units are weird with % values
- (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
Progress bar:
- Doesn't close properly on some Linux systems
- Focus requests change workspace when processing constantly (Linux systems)
MacOS bugs:
- Buttons {Yes,No,Cancel} listed backwards
- Record tab: Text of epoch number is too big
- Colormap menus: Do not work well on compiled MacOSX 10.9.5 and 10.10
in_bst_data_multi: If trials have different sizes, output is random (the one of the first file)
Canolty maps computation: Fix progress bar

Geeky programming details

bst_bsxfun: After 2016b, we can use directly the scalar operators (./ .* ...) instead of bsxfun. Update bst_bsxfun to skip the use of bsxfun when possible.
Interface scaling: Rewrite class IconLoader to scale only once the icons at startup instead of at each request of an icon (might improve the speed of the rendering of the tree)
Hide Java panels instead of deleting them
Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel"
Interpolations: Use scatteredInterpolant, griddedInterpolant, triangulation.nearestNeighbor (2014b)
bst_warp and channel_project: Use tess_parametrize_new instead of tess_parametrize
Shared kernels: "get bad channels" operation in a different way (reading all the files is too slow)
Optimize bst_get:
- Now study and subject have necessarily the same folder name
- Replace big switch with separate functions
Fix all the 'todo' blocks in the code

-  ⇤ ← Revision 204 as of 2016-03-11 21:52:24 → 
  Size: 20970
  Editor: FrancoisTadel
  Comment:
+   ← Revision 467 as of 2020-07-09 13:20:53 → ⇥
  Size: 25991
  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 6:
-== Current topics ==
==== Source modeling ====
 * Implementation of a new unified minimum norm/beamformer framework (work in progress)

==== Statistics ====
 * Implementation of new parametric and non-parametric tests (work in progress)

==== Documentation ====
 * Standard workflows for different types of data and experiments (work in progress)

==== Functional connectivity ====
 * Significance thresholding of the connectivity matrices (not started)

==== Computation ====
 * Removing the dependence to the Java interface to run in headless mode (not started)
 * Interacting directly with distributed computing systems  (not started)

<<BR>><<BR>>
-Line 26:
+Line 7:
- * 2D topographies:
  * Nicer topographies with circle around 2DDisc (similar to EEGLAB plots)
  * Standardized plots (using FieldTrip .lay files?)
  * Aligned on the midline at least
  * Contour lines sometimes messed up with Elekta recordings
  * Make the surface on which the values are interpolated simpler
+ * Sleep scoring wish list (Emily C):
  * Configurable horizontal lines (for helping detecting visually some thresholds)
  * Mouse ruler: Measure duration and amplitude by dragging the mouse.
  * Automatic spindle detector
  * https://neuroimage.usc.edu/forums/t/page-overlap-while-reviewing-raw-file-a-way-to-set-to-0/11229/13
 * RAW file viewer:
  * Downsample before filtering? (attention to the filter design)
  * Add parameter to make the visual downsampling more or less aggressive
  * Pre-load next page of recordings
  * Keep the filter specifications in memory instead of recomputing for every page
 * Bad trials: When changing the status of bad to good: remove the bad segments as well, otherwise it is not processed by processes like the PSD.
 * Review clinical recordings: Reduce the dimensionality of the data with a simple inverse problem, similar to what we do for the magnetic extrapolation ("Regional sources" in BESA, cf S Rampp)
-Line 33:
+Line 20:
- * Montages:
  * Allow to set the color for each channel separately
  * Allow the superposition of channels (NIRS)
  * Separators (" : MLC11" already works, could be just " : "), should add an empty space.
 * 2DLayout:
  * Use the same standard positions, too much space between sensors (Recordings + TF)
  * Overlay multiple conditions
  * RAW files: Doesn't work when changing page => need refresh of GlobalData.Preferences.TopoLayoutOptions.TimeWindow
  * Same shortcuts as the raw file viewer (right-click + move for gain)
  * Add support for montages
 * RAW file viewer:
  * Show easily the maximum value at the current time point
  * Pre-load next page of recordings
  * Events: Change the category of a selected event easily, instead of deleting/marking new
  * Events: advanced process for recombining.
  * Example:  http://www.erpinfo.org/erplab/erplab-documentation/manual/Binlister.html
 * Filtering:
  * Use short FIR filters instead of IIR for bandpass, to limit the ringing (bad for Hilbert as well)
  * Or allow the users to edit the LowStop parameter in bst_bandpass

 * Bad channels specified at the program level (for sites that have permanent bad channels: AS)
+ * Create heat maps: Maybe with matlab function heatmap?
 * BioSemi: Add menu "Convert naming system" to rename channels into 10-10 (A1=>FPz)
-Line 56:
+Line 24:
- * Start Brainstorm without Java (-nodesktop)
 * Allow FieldTrip functions in compiled version
 * Generalize the user of the units (field .Units): Rewrite processes to save the units correctly
+ * Add a warning when computing a forward model with > 100000 sources (check selection)
 * Snapshot: Save as image / all figures (similar to Movie/all figure)
 * Generalize the use of the units (field .DisplayUnits): Rewrite processes to save the units correctly
-Line 61:
+Line 29:
-  * Create a colormap similar to MNE, where extrema are bright
-Line 63:
+Line 30:
- * Open new figures as tab (docked in the Figures window)
-Line 65:
+Line 31:
- * Removing all the CTRL and SHIFT in the keyboard shortcuts
 * Display warning before opening files that are too big
-Line 68:
+Line 32:
+ * Contact sheets & movies: use average of time windows instead of single instants, for each picture.
 * Contact sheets: Allow explicit list of times in input (+ display as in MNE-Python with TS)
 * Display CTF coils: Show discs instead of squares
 * Use boundary() instead of conhull() in all the display functions (ie. 2DDisc)

 * Progress bar: Add a "Cancel" button
 * Error message: Add a link to report directly the bug on the forum
 * Reorganize menus (Dannie's suggestion): {{attachment:dannie_menus.png||width="382",height="237"}}
-Line 70:
+Line 42:
- * Thresholding the connectivity matrices
 * Stat tests on connectivity measures
 * Check why our Hilbert implementation has huge edge effects
 * Connectivity on unconstrained sources: how to group the three orientations?
 * Connectivity based on band limited power (Sylvain):
  * Compute Hilbert/Bandpass + correlation of the envelopes
  * Bandpass envelopes before computing correlations?
  * Compute Hilbert(sensors) and then project to source space?
 * Multi-tapers?
+ * Thresholding and stat tests the connectivity matrices
 * Connectivity on unconstrained sources: "Default signal extraction for volume grids should be the time series of  the first principal component of the triplet signals after each has  been zero-meaned" (SB)
 * Display of connectivity graphs:
  * Display as straight lines
  * Recode 2D graphs
  * 3D display with anatomical constrains
  * Display using real position of EEG electrodes
 * Use new band-pass filters in bst_connectivity ('bst-hfilter' instead of 'bst-fft-fir')
 * Matrix view of NxN graphs: Add legend of the elements along X and Y axis
 * Weighted Phase Lag Index (WPLI)
-Line 90:
+Line 63:
-  * Average cross-spectra instead of concatenating epochs (to avoid discontinuities)
 * Granger:
  * Crashes sometimes: improve stability
  * Re-write and optimize code
  * Add progress bar
+  * Average cross-spectra instead of concatenating epochs (to avoid discontinuities)<<BR>>Explore inter-trial approaches (Esther refers to chronux toolbox)
 * Granger: Check for minimum time window (Esther: min around 500-1000 data points)
-Line 101:
+Line 71:
- * PAC:
  * Add input TF , to disconnect TF decomposition and PAC computation (Peter)
  * Refine frequency vector of low frequencies
  * How many central frequencies to use in bst_pac?
  * Change filters: no chirplet functions
  * bst_freqfilter: Use nfcomponents like in bst_pac
  * Esther recommended a larger frequency binning of the PAC estimation
  * PAC maps: Display all sensors at once (like TF and DynamicPAC)
+  * Add warning when running of short windows (because of filters)
-Line 110:
+Line 73:
- * Other metrics:
  * Coherence by bands: bst_coherence_band_welch.m
  * Granger by bands: bst_granger_band.m
  * Inter-trial coherence
-Line 118:
+Line 77:
- * Optimize pipeline editor speed: Opening the window and the showing menu "Add process" are slow
+ * Decoding/Classifiers: Implement Dimitrios and scikit-learn algorithms
 * Allow processes in Python and Java
 * Add MNE-Python functions:
  * scikit-learn classifiers
  * Implement data exchange with MNE-Python: write FIF files from Brainstorm and/or pass python objects in memory instead of FIF files
  * https://neuroimage.usc.edu/forums/t/best-way-to-export-to-mne-python/12704/3
  * SSS/tSSS cleaning
  * Reproduce other tutorials / examples
  * Change the graphic renderer from Matlab
 * Add FieldTrip functions:
  * ft_sourceanalysis:
   * Check noise covariance
   * Check all the options of all the methods
   * Single trial reconstructions + noise covariance?
   * Filters?? http://www.fieldtriptoolbox.org/example/common_filters_in_beamforming
   * Beamformers: Save ftSource.avg.mom <<BR>>http://www.fieldtriptoolbox.org/workshop/meg-uk-2015/fieldtrip-beamformer-demo
   * http://www.natmeg.se/ft_beamformer/beamformer.html
   * http://www.fieldtriptoolbox.org/tutorial/beamformingextended
   * Baseline? Two inputs?
  * ft_prepare_sourcemodel: Compute MNI transformation (linear and non-linear) => Peter
  * ft_prepare_heamodel: Add support from BEM surfaces from the Brainstorm database
  * Freqanalysis: ITC
  * ft_read_atlas('TTatlas+tlrc.BRICK');
  * ft_volumereslice: http://www.fieldtriptoolbox.org/faq/how_change_mri_orientation_size_fov
  * ft_freqanalysis
  * ft_combineplanar
 * Optimization:
  * Use CUDA for speeding up some operations (filtering, wavelets, etc)
  * Use Matlab Coder to optimize: Wavelets, bandpass filter, sinusoid removal
 * Pipeline editor:
  * Bug: After "convert to continuous", the time of the following processes should change
  * Add loops over subjects/conditions/trial groups
  * Events: Allow selection from a drop-down list (similar to option "channelname" in panel_process_selection)
  * When computing sources from the pipeline editor: doesn't reselect the  options if you click twice on "edit" (works  for minnorm, but not for  lcmv)
 * ITC: Inter-trial coherence (see MNE reports for group tutorial)<<BR>>http://www.sciencedirect.com/science/article/pii/S1053811916304232
-Line 121:
+Line 114:
+  * Why doesn't the ICA process converge when using 25 components in the EEG tutorial?
  * Add an option to resample the signals before computing the ICA decomposition
-Line 122:
+Line 117:
+  * Export IC time series (and then compute their spectrum): solves the problem above
-Line 123:
+Line 119:
+  * Use faster methods (MNE-Python?)
-Line 127:
+Line 124:
-  * Use FastICA (algo crashing)
  * Understand why EEG/Epilepsy tutorial data crashes if we don't limit the number of components
  * Add components preselection: Correlation with EOG/ECG
-Line 132:
+Line 126:
- * Use Matlab Coder to optimize some processes: Wavelets, bandpass filter, sinusoid removal
 * Allow processes in Python and Java
+  * ICA+machine learning: https://www.ncbi.nlm.nih.gov/pubmed/28497769
  * Automated artifact rejection: https://arxiv.org/abs/1612.08194
  * Use EYE-EEG: EEGLAB toolbox for eye-tracker guided ICA (Olaf Dimigen): http://www2.hu-berlin.de/eyetracking-eeg/
 * Other EEGLAB functions:
  * Step function detection: https://github.com/lucklab/erplab/wiki/Artifact-Detection:-Tutorial
-Line 136:
+Line 133:
-  * Show where the attenuation is projected:<<BR>>(sum(IK,2)-sum(SSP(k,:)*IK,2)./sum(IK,2)
 * Bandpass:
  * Offer option: bst_bandpass_fft / bst_bandpass_filter
  * Rewrite without the forced low-pass filter at Fs/3
  * Show warning when using inappropriate high-pass filter (precision too high)
  * Use FIR filter
-Line 148:
+Line 139:
-  * Allow running on source files attached to continuous files (needs a lot of rewriting)
+  * Allow display of Avg+StdErr
-Line 150:
+Line 141:
- * Band-limited power envelope
 * Reports:
  * Save as HTML / PDF
 * Pipeline editor:
  * Add loops over subjects/conditions/trial groups
-Line 156:
+Line 142:
-  * Induced calculation: Avg(Power(TF(trials - Avg(Trials)))): <<BR>>Add option "Remove evoked response from each trial"
  * Standardize using: diff before calculation + cumsum (checkbox "flatten data")
  * Frequency bands: extended syntax (ex: [2 3 4], 10:5:90, ...)
  * Display logs as negative
  * Difference of power displayed in log: problems (Soheila)
+  * Optimization: bst_timefreq (around l.136),  remove evoked in source space: Average should be computed in sensor  space instead of source space (requested by Dimitrios)
  * Short-time Fourier transform: http://www.mikexcohen.com/lectures.html
  * Matching pursuit: http://m.jneurosci.org/content/36/12/3399.abstract?etoc
  * Bug: Display logs as negative
  * Bug: 3D figures: Colormaps with "log" option doesn't work
  * Bug: Difference of power displayed in log: problems (Soheila)
-Line 167:
+Line 154:
-  * 3D figures: Colormaps with "log" option doesn't work
-Line 169:
+Line 155:
-  * TF on scouts: Add progress bar when extracting all the scouts time series (can be long)
+  * When normalizing with baseline: Propagate with the edge effects marked in TFmask
  * Allow baseline normalization of files computed with time bands
  * Allow running TF on montages
  * Review continuous files in time-frequency space (for epilepsy)
  * Bug when computing TF on constrained and unconstrained scouts at the same time (in mixed head models for instance): uses only the constrained information and doesn't sum the 3 orientations for the unconstrained regions.
-Line 173:
+Line 163:
-  * Allow the detection on differences of signals (bipolar montages)
 * Co-registration of MEG runs:
  * SSP: Group projectors coming from different files
  * Finish validation of the method
  * Apply to continuous recordings for correcting head movements
 * Resample continuous files
 * Other processes:
  * Moving average
  * Max
  * Median
  * Significance test (Dimitrios, Leo)
  * Spatial smoothing: check / document parameters
 * Contact sheets & movies: use average of time windows instead of single instants, for each picture.
 * Optical flow
+ * Events detection: Add option "std" vs "amplitude"
-Line 188:
+Line 165:
+  * EEGSourceSim: https://www.sciencedirect.com/science/article/pii/S0165027019302341
-Line 194:
+Line 172:
- * Sort files by comment
-Line 198:
+Line 175:
- * Add notes in the folders (text files, visible as nodes in the tree)

 * Screen captures: save straight to the database
-Line 205:
+Line 178:
+ * Auto-save:
  * protocol.mat can be too big: do not store the results links in it (and recreate when loading)- http://neuroimage.usc.edu/forums/t/abnormally-slow-behavior/2065/10

  * Improve auto-save: add tracking file next to protocol.mat, do not save all the time, only when closing app, and reload protocol at stratup if tracking file is still there
-Line 214:
+Line 192:
+ * Various initiatives: http://samirdas.github.io/Data_sharing.html#/
-Line 216:
+Line 195:
+ * Sensitivity maps: https://mne.tools/stable/auto_examples/forward/plot_forward_sensitivity_maps.html
 * Reproduce results in "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
 * Use eLORETA instead of sLORETA? <<BR>>https://neuroimage.usc.edu/forums/t/compute-eeg-sources-with-sloreta/13425/6
  * "eLORETA  algorithm  is  available  in  the  MEG/EEG Toolbox of Hamburg (METH)": https://www.biorxiv.org/content/biorxiv/early/2019/10/17/809285.full.pdf
 * Point-spread and cross-talk functions (code in MNE-Python):
  * https://www.biorxiv.org/content/biorxiv/early/2019/06/18/672956.full.pdf
  * https://github.com/olafhauk/EEGMEGResolutionAtlas
 * Dipoles:
  * Project individual dipoles files on a template
  * panel_dipoles: Doesn't work with multiple figures
 * Project sources: Very poor algorithm to project sub-cortical regions and cerebellum (algorithm to fit surfaces should be imrpoved)
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Menu Sources > Maximum value: Doesn't work with volume or mixed head models
-Line 217:
+Line 209:
-  * Project to templates (scouts or source maps)
  * Create scout form maximum doesn't work (menu Sources > Max value)
  * Display in MRI doesn't work
  * Smooth display: do not smooth subcortical structures
  * Export as .nii volume: doesn't work
 * Dipoles:
  * panel_dipoles: Doesn't work with multiple figures
  * Read easily dipole coordinates: Click on one selects it and open the panel Get coordinates
 * Panel Get coordinates: Add button "find maximum"
 * Stenroos 2014 paper: Include the following methods
  * Inner and outer skull surfaces generator from FieldTrip (needs SPM)
  * Nolte corrected-sphere model (good model re:Alex)
  * Fast BEM models
 * Visualize Beamformer results:
  * Read CTF SAM .svl
  * Display as layers in the MRI viewer
 * Unconstrained sources:
  * Stat and connectivity: what to do? (re-send email John+Sylvain)
 * Overlapping spheres: improve the estimation of the spheres for the frontal lobes
+  * Set loose parameter from the interface
  * Bug when displaying interpolated in MRI viewer
-Line 237:
+Line 212:
-  * Test volume sources with all the subsequent processes (timefreq, stat...)
-Line 240:
+Line 214:
- * 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
 * Calculate ImagingKernel * Gain for a scout
 * Beamformers from FieldTrip (LCMV, SAM)
 * Time-frequency beamformers:
  * Band-pass everything in different frequency bands + Source estimation + TF
  * Ask data to Sarang where he sees effects that cannot be extracted with MN followed by TF
 * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
 * BEM: Fix unstable results when one vertex is too close from the layers (5mm ?)
 * Hui-Ling beamformers:
  * More explanations about what is in NAI and Spatial filters
  * Explain that is this is better to study effects extended in time (Ntime > Nsensors)
  * Group LCMV+MCB
  * Condition LEFT median nerve: very bad results
-Line 264:
+Line 217:
+ * Panel Get coordinates: Add button "find maximum"
 * BEM single sphere: Get implementation from MNE
 * Unconstrained sources:
  * Stat and connectivity: what to do? (re-send email John+Sylvain)
 * Sources on surface: Display peak regions over time (time = color) => A.Gramfort
 * Process "Extract scouts time series": Add PCA option (replace isnorm with choice PCA/Norm)
 * Add eyes models to attract eye activity
 * Display source maps on a flat 2D cortex projection (Mollweide projection): https://neuroimage.usc.edu/forums/t/source-model-display-and-output/13940/5
-Line 266:
+Line 227:
- * MNI coordinates: Extend to non FreeSurfer volumes (BrainSuite volumes that are not 256x256x256)
 * Project all sub-cortical structures to default anatomy (check code from Denis S)
 * Add cerebellum to default model generated with "Import FS anatomy"
 * Import MRIs with different resolutions: re-interpolate automatically
 * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
 * Warping: Scale option has to be fixed, it is currently very unstable
+ * '''CAT12''': Optimize interpolation of atlases (import is super slow...)
 * '''SimNIBS''': Replace HEADRECO with CHARM (headreco will be removed in SimNIBS 4)
 * Keep ASEG volume + display region name in MRI viewer
 * Multi-Scale Brain Parcellator (Lausanne2008):
  * [[https://github.com/sebastientourbier/multiscalebrainparcellatorhttps://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator|https://github.com/sebastientourbier/multiscalebrainparcellator]]
  * [[https://github.com/sebastientourbier/multiscalebrainparcellatorhttps://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator|https://hub.docker.com/r/sebastientourbier/multiscalebrainparcellator]]
  * https://multiscalebrainparcellator.readthedocs.io/en/latest/

 * MNI transformation: Use SPM non-linear MNI transformation y_...
 * Registration:
  * Getting electrode positions from 3D scanners: https://sccn.ucsd.edu/wiki/Get_chanlocs
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
  * Use the same registration for multiple recording sessions that have already re-registered previously (eg. with MaxFilter)
  * When linking multiple EEG recordings including 3D positions, do the registration only once and copy it to all the runs
  * Compute non-linear MNI registration instead of linear
  * Select and remove bad digitized head points before automatic coregistration
  * Load the MNE -transf.fif: http://neuroimage.usc.edu/forums/showthread.php?2830
 * MRI Viewer:
  * Pan in zoomed view (shift + click + move?)
  * Zoom in/out with mouse (shift + scroll?)
  * Ruler tool to measure distances
  * Display scouts as additional volumes
  * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix<<BR>>Or use inpolyhedron to get a surface mask and then erode it to get the volume envelope
  * Edit fiducials: Replace 6 text boxes with 1 for easy copy-paste (see fiducials.m)
  * Optimize computation interpolation MRI-surface (tess_tri_interp) => spm_mesh_to_grid
 * BrainSuite:
  * Add new labels to all BrainSuite anatomy templates
  * Use same colors for left and right for anatomical atlases
  * Use for volume coregistration (rigid / non-rigid)
 * FEM templates for different ages:
  * Pediatric head atlases: https://www.pedeheadmod.net/pediatric-head-atlases-v1-2/

  * https://iopscience.iop.org/article/10.1088/2057-1976/ab4c76
  * https://www.biorxiv.org/content/biorxiv/early/2020/02/09/2020.02.07.939447.full.pdf
  * John Richards: https://www.nitrc.org/frs/?group_id=1361
 * MRI to FEM mesh generation :<<BR>>
  * Process the FEM cortex/source space (either from CAT or SimNibs) and fit all the dipoles within the grey matter (important in the case where white matter and scf are considered) to acheive the Venant condition (also for other source models
-Line 275:
+Line 268:
+  * Sort scouts by region in process options
-Line 276:
+Line 270:
-  * Sort scouts by region in process options
 * Menu head model > Copy to other conditions/subjects (check if applicable first)
 * Generate mixed density surfaces
 * Optimize computation interpolation MRI-surface (tess_tri_interp)
 * Render surface envelope in the MRI as a thin line instead of the full interpolation matrix
+  * Project from one hemisphere to the other using registered spheres/squares (http://neuroimage.usc.edu/forums/t/how-to-create-mirror-roi-in-the-other-hemisphere/5910/8)
 * Parcellating volume grids: scikit-learn.cluster.Ward
-Line 282:
+Line 273:
- * Smooth surface: Fix little spikes due to irregularities in the mesh
 * Add eyes models to attract eye activity
+ * Surface>Volume interpolation: Use spm_mesh_to_grid
 * Bug: Hide scouts in the preview of the grid for volume head models
 * Geodesic distance calculations:<<BR>>https://www.mathworks.com/matlabcentral/fileexchange/6110-toolbox-fast-marching
-Line 286:
+Line 278:
- * Co-register MRI and CT for electrodes marking in the MRI Viewer
 * Import/export electrodes positions in MNI/SCS/MRI coordinates
 * Display SEEG+ECOG contacts at the same time
 * Problem of difference between RAS and TkRegRAS: http://neuroimage.usc.edu/forums/showthread.php?1958-SEEG-electrodes-and-subject-s-anatomy-are-not-alligned
+ * Electrodes models: Import / export
 * Contact positions: Import / set / detect
  * New option: Align on none|inner|cortex to replace ECOG-mid
  * Add history: Save modifications and transformations applied to the channel files (Marcel)
  * Project contact positions across subjects or templates (Marcel)
  * Add menu to import implantation channel file in imported recordings
 * SEEG/ECOG: Identify contacts in resected areas / identify ROIs for each contact
 * SEEG/ECOG: Identify contacts in a give anatomical region (volume scout, surface mesh, or label in a volume atlas) / allow extracting the signals from all the contacts in an ROI
 * Automatic segmentation of CT:
  * GARDEL: http://meg.univ-amu.fr/wiki/GARDEL:presentation
  * Arnulfo: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0511-6
  * MAP07 / SPM: https://www.epi.ch/_files/Artikel_Epileptologie/Huppertz_2_13.pdf
 * ECOG:
  * Project and display contacts on cortex surface should consider the rigidity of the grids: Contacts cannot rotate, and distance between contacts should remain constant across runs
  * Method for contacts projection: https://pdfs.semanticscholar.org/f10d/6b899d851f3c4b115404298d7b997cf1d5ab.pdf
  * ECOG: Brain shift: When creating contact positions on a post-implantation image, the brain shift should be taken into account for creating images of the ECOG contacts on the pre-op brain => iELVis (http://ielvis.pbworks.com/w/page/116347253/FrontPage)
 * Display:
  * Bad channels: Contacts greyed out instead of ignored (Marcel)
  * Display time in H:M:S
  * Display curved SEEG electrodes
 * Export list of contacts with a probability of anatomical regions from various atlases: https://neuroimage.usc.edu/forums/t/seeg-contacts-anatomical-location/14756
 * Detection CEEP stim artifacts: Use ImaGIN code ImaGIN_StimDetect
-Line 292:
+Line 302:
- * ANOVA: Use LENA functions(?)
+ * ANOVA:
  * Which functions to use?
  * Write panel similar to Process1 and Process2 to allow the
-Line 295:
+Line 307:
- * Problem t-test on unconstrained sources: (convert to flat + Z-score)
 * FieldTrip implementation:
  * Add logic of bad channels individually per sensor instead of removing completely all the channels that are marked as bad in at least one trial
 * Use SurfStat: Impements interesting things, like an analytical cluster-based p-value correction (Random-field theory which is used in SPM) - Peter
 * PLS: Partial Least Squares
 * In Stat tab: Correction by temporal extension (display only if effect longer than a given input in ms)
+ * Quality control before statistics, on condition averages across subjects:<<BR>>mean(baseline)/std(baseline): shows bad subject quickly.
 * Use SurfStat: Impements interesting things, like an analytical  cluster-based p-value correction (Random-field theory which is used in  SPM) - Peter
 * Export to R or SPSS for advanced stat
-Line 303:
+Line 312:
+ * Bug import multiple files: use same "time" for all files
 * BIDS import:
  * Read real fiducials
  * Read associated empty room
  * Test all the BIDS examples
 * BIDS Export:
  * Add events ts, channel tsv, EEG, iEEG

 * '''XDF import''': Use FieldTRip or the EEGLAB plugin, contact Martin Bleichner (Oldenburg)<<BR>>https://github.com/sccn/xdf/blob/master/xdf_sample.xdf
 * DICOM converter:
  * Add dcm2nii (MRICron)
  * Add MRIConvert
 * FieldTrip: Import/Export time-frequency:
  * Export: http://neuroimage.usc.edu/forums/t/export-time-frequency-to-fieldtrip/1968
  * Import: http://neuroimage.usc.edu/forums/t/import-time-frequency-data-from-fieldtrip/2644
-Line 304:
+Line 328:
+  * Use reader from MNE-Python: mne.io.read_raw_kit  (doesn't require Yokogawa slow library)
-Line 306:
+Line 331:
-  * Validate with phatom recordings that noise compensation is properly taken into account
  * References at too far from the head sensors in Marseille 4D system
+  * Validate with phantom recordings that noise compensation is properly taken into account
-Line 309:
+Line 333:
- * FieldTrip integration:
  * Import/Export continuous recordings
  * Export trials with a trial definition: http://neuroimage.usc.edu/forums/showthread.php?2213
+  * 4D phantom tutorial (JM Badier?)
-Line 315:
+Line 337:
+  * XLTEK: https://github.com/danielmhanover/OpenXLT
  * Persyst .lay: https://github.com/ieeg-portal/Persyst-Reader
  * Nervus .eeg: https://github.com/ieeg-portal/Nervus-Reader
  * Biopac .acq: https://github.com/ieeg-portal/Biopac-Reader
  * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
-Line 316:
+Line 343:
- * EEGLAB import:
  * 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
+ * BST-BIN: Add compression to .bst
-Line 321:
+Line 345:
- * gTec EEG recordings: Read directly from the HDF5 files instead of the Matlab exports.
 * Use new Matlab functions readtable/writetable (2006b): for Excel and text files
+ * SPM .mat/.dat: Fix the import of the EEG/SEEG coordinates
 * Get acquisition date from files: Missing for 4D
 * Support for OpenJData / JNIfTI: https://github.com/brainstorm-tools/brainstorm3/issues/284
-Line 325:
+Line 350:
+ * Tutorial OMEGA/BIDS:
  * Update the organization of derivatives folder (same for ECOG tutorial)
  * Add review of literature for the resting state MEG
  * Download example datasets directly from the OMEGA repository
 * New tutorials: <<BR>>
  * Other public datasets: [[https://github.com/INCF/BIDS-examples/tree/bep008_meg|https://github.com/INCF/BIDS-examples/tree/bep008_meg/]]
  * Rat PAC + high gamma (Soheila)
  * EEG/research
  * FieldTrip ECOG tutorial: http://www.fieldtriptoolbox.org/tutorial/human_ecog
  * FieldTrip cortico-muscular coherence tutorial: http://www.fieldtriptoolbox.org/tutorial/coherence
  * Reproduce tutorials from MNE-Python: https://martinos.org/mne/stable/tutorials.html
  * Cam-CAN database: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/<<BR>>(download new datasets, including maxfiltered files and manual fiducial placements)
  * MEG steady-state / high-gamma visual / frequency tagging
  * BIDS-EEG example datasets
  * Reproduce results from "Simultaneous human intracerebral stimulation and HD-EEG, ground-truth for source localization methods": https://www.nature.com/articles/s41597-020-0467-x
 * Stand-alone ICA tutorial

 * Move all the files to download to the cloud for faster download everywhere in the world
 * Provide secure way of sending password over HTTPS for:
  * Account creation
  * Forum exchanges
  * org.brainstorm.dialog.CloneControl
-Line 326:
+Line 373:
- * Reference tutorials on Google scholar + ResearchGate
 * Cleaning threads on the forum
 * Add Help buttons and menus (in popups, dialog windows...) => Links to the website.
 * Finish existing tutorials:
  * EEG/Epilepsy: Rewrite scripts + update contents (with Geneva2015 walkthrough)
  * Dipoles
  * Group MEM/Epilepsy + Epilepsy tutorials
 * New tutorials:
  * MEG steady-state / high-gamma visual
  * Intra-cranial recordings
  * MEG connectome (impossible without the head shapes)
  * Scrambled faces (SPM/MNE-Python)
  * Coherence (cortico-muscular ?)
  * Co-register MEG runs (Beth)
 * Missing in the introduction tutorials:
  * Volume scouts
  * Sources: Model evaluation (by simulating recordings)
  * Time-frequency: Description of "log freq scale" option
  * Modify a structure manually: Export to Matlab/Import from Matlab
  * File manipulation: file_short, file_fullpath, in_bst_*...
  * Description of all fields in MRI and surfaces
 * Script tutorials: ask what folder contains the tutorial datasets
 * Missing in tutorial "Export to SPM": Add section "Compare with Brainstorm"
 * Missing in page "Cite Brainstorm": Add all the methods used in the software
+ * Count GitHub clones in the the download stats
 * Deface the MRIs of all the tutorials
 * Clean up the wiki:
  * Remove all the wiki pages that are not used
  * Check all the links in all the pages
  * Check that all the TODO blocks have been properly handled
  * Remove useless images from all tutorials
  * Update page count on the main tutorials page
-Line 352:
+Line 383:
- * Screen capture:
  * Bug on Win8/Win10: doesn't capture the correct part of the screen
  * Window managers with fading effect: captures the top window
+ * MacOS 10.14.5 (Mojave):
  * Toggle buttons do not show their status
  * Panel Record: Text is too large for text boxes
-Line 359:
+Line 390:
-  * (TF) Images are too far apart with EEG 20 channels
  * (time series) Sometimes the lines are not visible
  * (time series) Does not work when DC offset is not removed
+  * (TF) Units are weird with % values
  * (TF) Difficult to navigate in frequencies: Scaling+changing frequency resets the scaling
-Line 369:
+Line 399:
- * Matlab bugs:
  * Interface looks small on screens with very high resolutions: Reduce the resolution
  * Out of memory errors on Win 32bits (restart Matlab)
  * Matlab 2014b bug with rmdir/movefile: Enter but never returns from the call
 * Event markers are not visible anymore with the sequence: Open MEG, open EOG, close MEG
-Line 375:
+Line 400:
- * Edit scout in MRI: small modifications cause huge increase of the scout size
-Line 377:
+Line 401:
- * Change of default anatomy does not reset the interpolation matrices in all the subjects.
  * After projecting sources once from subject to default anat, the interpolation is saved and not updated. Interpolations need to be removed manually before projecting again on a new template.
-Line 381:
+Line 403:
+ * bst_bsxfun: After 2016b, we can use directly the scalar operators (./ .* ...) instead of bsxfun. Update bst_bsxfun to skip the use of bsxfun when possible.
 * Interface scaling: Rewrite class IconLoader to scale only once the icons at startup instead of at each request of an icon (might improve the speed of the rendering of the tree)
-Line 382:
+Line 406:
+ * Processes with "radio" and "radio_line" options: Replace with "radio_label" and "radio_linelabel"
-Line 388:
+Line 413:
- * 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 394:
+Line 414:
- * 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
 * Optimize MRI viewer with patch() instead of image()

Software

Users

Development

What's next

Recordings

Interface

Connectivity

Processes

Database

Distributed computing

Source modeling

Anatomy

ECOG/SEEG

Statistics

Input / output

Distribution & documentation

Current bugs

Geeky programming details