enhancement

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• 6 - add cfg.inputfile and cfg.outputfile to all fieldtrip functions
• 13 - include bitsi from google code repository to fieldtrip/external
• 16 - do not redraw topoplot of component when scrolling through trials
• 21 - select channels/components (as artifacts) in databrowser
• 26 - implement cfg.precision for all functions
• 34 - add elliptic filter type to preproc_xxfilter
• 53 - redesign the filetype detection
• 54 - separate conversions and fixes from checkdata
• 57 - the fieldtrip logo should be available on the wiki
• 89 - use bwlabeln from spm8 as alternative to image processing toolbox
• 97 - if the user specifies cfg.trials=[] this should result in no trials being processed. Now all trials are processed
• 100 - Conversion error in ft_sourcestatistics
• 102 - cfg.inputfile for ft_prepare_bemmodel with 3 input options
• 103 - with addition of optional cfg.inputfile ylim error
• 104 - topoplotTFR cannot correctly refer to topoplotER with cfg.inputfile
• 108 - reading in of ctf-header with headerformat ctf_ds outputs a lot of stuff to the screen, making it slow
• 112 - missing figures megrealign
• 113 - missing figures dipole fit
• 114 - Symmetric dipoles example scripts need updates and illustration
• 115 - ft_prepare_mesh not robust in dealing with inputfile
• 117 - cfg.channel no longer being used in ft_multiplotTFR
• 118 - make ft_prepare_layout detect identical channel locations
• 119 - plotting functions renamed without fixing the ft_ prefixes in the code
• 123 - statfun_depsamplesT and statfun_actvsbslT cannot manage nans
• 124 - different linestyles for multiple lines in the same plot
• 128 - options for overlapping trials?
• 129 - non prefixed ft_xxx functions on wiki
• 130 - ensure robust behaviour for freqanalysis when user specifies both cfg.channel and cfg.channelcmb
• 132 - sobi hsould be added to external/eeglab
• 133 - ft_connectivityanalysis averaging trials bug
• 137 - implement udpserver
• 140 - busy peerslave should announce the memreq of the job instead of the memavail
• 141 - there should be a mechanism for logging the output of the command-line peerslaves
• 142 - peer should announce timavail=0 for zombie and master
• 145 - documentation in peer.m should be more general introduction
• 147 - improve help in functions by linking to wiki documentation
• 152 - pass global variables to peerslave
• 153 - implement refuseuser, refusehost, refusegroup
• 154 - add a description field in the host package
• 158 - improve scheduling in peerfeval
• 161 - Test Data for 4D bivariate plotting enhancement
• 173 - nice level
• 174 - implement EDF and GDF format in ft_write_data
• 180 - make ft_multiplotXXX and ft_topoplotXXX robust against subset of all channels in input, in case of connectivity data
• 183 - include job number in rethrown error inside peerget
• 202 - ft_databrowser: add showing of events in vertical view mode
• 203 - add ft_denoise_pca to the release of fieldtrip
• 208 - ft_ prefix inverse module
• 224 - rename and documentation of fieldtripdefs.m
• 248 - add mini-spm8 version to fieldtrip/external
• 256 - ft_clusterplot cannot plot TFR clusters
• 273 - add support for channel-selection in multiplotTFR
• 274 - add support for channel-selection in topoplotER/TFR
• 276 - add support for channel-selection to multiplotCC
• 284 - make implementation for specest_convol (previously tfr)
• 285 - make implementation for specest_wavelet (previously wltconvol)
• 286 - make implementation for specest_hilbert
• 287 - update FAQs on wiki for all specest_functions/methods
• 300 - link the fieldtrip bugzilla to the debian bugzilla
• 306 - too many resubmissions with small nr of collected jobs
• 312 - statistics_* should be ft-prefixed
• 316 - the public functions should be ft_ prefixed
• 320 - ft_spike_sub_crossx.mexmaci should not be in main directory
• 321 - the spike plotting functions should be renamed ft_spikeplot_xxx for consistency with the other plotting functions
• 348 - make spatial clustering on 2D 'meshes' more general
• 369 - No horizontal scaling possibility in ft_databrowser on noncontinuous data
• 380 - implement ztransform/standardize in rejectvisual
• 393 - implement a warningonce function
• 395 - create faq on 'what to do when my script does not work anymore, and it worked perfectly fine in 2003'?
• 405 - Establish a closer distinction / relation between ft_databrowser and ft_rejectvisual
• 433 - improve search option on mailing list
• 441 - implement ft_realtime_signalrecorder
• 442 - the cfg defaults for the mri and meg headlocalizers should be specific to our lab computers
• 443 - merge ft_poll_buffer into ft_read_data
• 444 - move the serPort in ft_omri_quality with ft_write_event
• 445 - move decoding of omri SAP/nifti into fileio/private
• 446 - reorganize the development/realtime documentation
• 456 - Add EGI MFF data format
• 487 - warning message is too long
• 489 - savevar (i.e. cfg.outputfile) should use an uncompressed format if the variable is small
• 496 - the "properties" code is obsolete and should be removed from the buffer c-library
• 506 - Suggestion for reading gdf events
• 529 - ft_preprocessing should support padding for continuous data in-memory
• 530 - check description of design matrix conditional on required statfun
• 532 - implement a ft_crossfreqanalysis function
• 542 - Speed up ft_multiplotER
• 580 - ft_filetype.m contains references to the nonexistent and mysterious "F.C. Donders Centre"
• 602 - questions in tutorials should have an answer
• 621 - creating a brainmask in MNE pipeline is not in FT style
• 630 - ft_databrowser redraws everything when marking new artifacts
• 634 - add spherical spline interpolation to ft_channelrepair
• 635 - ft_channelrepair should use cfg.neighbours instead of cfg.neighbourdist
• 637 - ft_appenddata should be extended to also support appending timelock, freq and source data
• 640 - make trialfun, statfun and browsefun behave consistently
• 644 - ft_channelrepair does not work on missing channels
• 645 - Increase the speed of reading in xml files, Anyone an idea how to??
• 646 - electroderealign should be improved for yokogawa/MEG and should be renamed into sensorrealign
• 648 - ft_uilayout and layoutgui should perhaps be merged
• 656 - ft_timelockanalysis: output should have a dimord consistent with its fields
• 664 - private/sensortype.m should be deprecated
• 683 - ft_movieplot for Time-frequency analysis
• 694 - Suggestion to use (Matlab) syntax highlighting in <code>
• 695 - development: improve visualization of MNE source reconstruction results
• 698 - development: code is not in FT style
• 699 - development: group analysis and statistics on MNE source reconstruction
• 707 - implement a ft_connectivityplot function
• 708 - re-implement ft_timelockstatistics
• 709 - create ft_connectivity_xcorr
• 710 - create faq on the representation of bivariate frequency domain data
• 711 - implement an interface to the graph analysis toolbox by rubinov/sporns/kötter
• 712 - build in the non-homogeneous smoothing at the source level
• 721 - patch for rejectvisual_summary.m to visually show which trl/chan were removed
• 722 - enable data cursor mode in rejectvisual_summary
• 733 - demo_buffer.c (which is buffer.exe) has an unused 1st argument
• 745 - similar to cfg.trials and cfg.channel, functions should get an option cfg.latency
• 747 - cfg.design and design are both possible inputs in stat* functions
• 748 - close buffer cleanly
• 765 - singleshell head model should foresee a smoothing function
• 779 - ft_multiplotER : the sensors are out of the schematic head
• 780 - filter instability
• 784 - UI update to ft_rejectartifact
• 790 - UI improvements to rejectvisual_summary
• 797 - documentation on mex files needs to be updated
• 800 - Create and optimize templates for neighbourselection
• 809 - Suggestion: Let neighbourselection calculate distances for neighbours
• 818 - If no layout is given, it could be estimated using ft_senstype(data)
• 820 - cfg.vol should not be required input to ft_sourceanalysis
• 833 - minimumnormestimate should work with lambda in an interpretable range
• 841 - use consistent british or american english throughout
• 849 - convention of 'directionality' in spectral transfer function is swapped wrt the other connectivity metrics
• 856 - allow user to specify critical time window for ft_reject_artifact
• 872 - implement and test statfun_glm
• 875 - add gray and yellow to colorscheme
• 890 - create mat-files for the mostly used acquisition systems to better reflect the features of the channel positions/ outline
• 929 - xxx2fieldtrip function user interface should be made more consistent
• 942 - ensure consistent structure of the main ft_functions
• 951 - the main plotting functions have inconsistent return values
• 952 - functions that return cfg should check on nargout
• 1003 - feature: use ft_headmodelplot without grad/elec
• 1010 - layout of subplots in ft_topoplotER
• 1032 - make the check on the existence of the file in ft_read_xxx consistent
• 1034 - private/spikesort has a non-standard way of debugging
• 1038 - the reading functions can support tgz and zip datasets, unzip on the fly
• 1045 - add ft_checkconfig option: forbiddenval or unusedval
• 1064 - use the gradient function in ft_preproc_derivative instead of diff
• 1073 - TIP of the Day: "Do you know..." any?
• 1088 - ft_volumelookup behaves inconsistently w.r.t. the handling of the cfg options
• 1090 - cfg.elec, cfg.elecfile etc have to be documented consistently
• 1092 - discuss in the FT meeting how to do cfg tracking for definetrial and artifact_xxx
• 1095 - negative trialpadding in ft_artifact_zvalue
• 1097 - discuss the remove flag in ft_redefinetrial, possibly reimplement
• 1099 - fixdipole should be done in ft_checkconfig instead of main FT functions
• 1114 - make a dependency table for compat and ensure that all dependencies are appropriate
• 1122 - to discuss: would it make sense to provide a set of template 3D grids in the fieldtrip release?
• 1127 - implement variable loading consistently
• 1128 - collapse multiple calls of ft_checkconfig into one
• 1131 - Should ft_checkconfig also deal with fixdipole?
• 1135 - Remove neighbourtemplates for MEG systems that are based on 2D layouts?
• 1141 - extend the ft_analysisprotocol function with reports on the callinfo
• 1142 - the cfg history is not fully kept in e.g. the artifact handling
• 1156 - Collaborate with TOBI on acquisition interoperability
• 1157 - fileio/README describes missing files base64.{c,h}
• 1161 - we need a drop-in replacement for the randperm function
• 1169 - can low-level fileio know how to read only requested channels?
• 1173 - Google Code page: SVN repository
• 1183 - boolean cfg options should need consistent values to be true or false
• 1184 - ft_timelockgrandaverage cannot handle variables that lack an 'avg' field
• 1185 - ft_connectivityplot should be extended to also support time and time_freq
• 1186 - Extend the plotting tutorial with the connectivity plotting functions
• 1191 - allow users to disable mem and time usage messages.
• 1195 - integrate fieldtrip spike toolbox with mclust
• 1196 - conversion between spike and raw data representation should be done by ft_checkdata
• 1198 - add waveform functions to fieldtrip
• 1199 - demeaning in ft_specest_mtmconvol should be performed in time-resolved fashion
• 1205 - implement cfg.seed input to ft_componentanalysis
• 1206 - documentation ft_datatype_raw incomplete
• 1211 - ft_chantype should be made faster
• 1213 - request: shut off fprintf if cfg.feedback='none' in ft_databrowser?
• 1222 - there are two copies of ft_prepare_bemmodel
• 1230 - suggestion for enhancement of ft_rejectvisual
• 1234 - Build script to list which compiled (e.g. mex, realtime) files are outdated
• 1235 - ft_selectdata (ft_selectdata_new) should retain sampleinfo when possible
• 1240 - ft_read_data call ft_filetype over and over again in call to ft_getopt
• 1256 - because of caching of data and header information wrong data can be read
• 1269 - documentation: "pitfalls/procedures of source analysis; define 'virtual sensor' "
• 1274 - complete the CSP implementation in ft_componentanalysis
• 1289 - plotting functions could change the figure window title
• 1291 - consider to use addpref/getpref instead of the global ft_default
• 1301 - Organize bugs to work on during bug-binge 20120201
• 1302 - extend the regression testing framework with old versions
• 1330 - y-axis of z-scored rejectvisual plots says /muV or Tesla instead of z-score
• 1331 - more informative job id
• 1351 - checksize in checkconfig takes ages on a grandaverage
• 1358 - functional sourcedata needs to be interpolated before plotting...
• 1365 - extend the "spm double installation" path check to other toolboxes
• 1367 - slow speed of niftii file creation using sourceinterpolate.m for 4D datasets
• 1375 - sourceinterpolate help should be merged
• 1376 - cfg options should obey to (updated) code guidelines
• 1393 - extend example script for LCMV, for general time-domain source analysis
• 1399 - channel selection mismatches displayed name in ft_reject_visual in summary mode
• 1401 - Add ft_artifact_shiftdetect
• 1404 - implement support for the neurosim spikes and signals file format
• 1406 - ft_progress could print the progress in place, rather than use newlines
• 1407 - finalize the egi_mff implementation
• 1442 - add cfg.channel in ft_prepare_neighbours, and add warning when no neighbour is found
• 1445 - document grad structure
• 1486 - improve artifact detection and rejection for unstable acquisition systems
• 1488 - ft_specest_mtmfft should support variable number of tapers over frequencies
• 1497 - provide more pointers to good reference literature
• 1499 - ft_singleplotER does not plot statistical error
• 1502 - forbid fields in cfg that are not used
• 1524 - Add support for neuroscan surface meshes *.tri
• 1528 - implement test script based on the various EEG data that is available
• 1549 - Add patch for ft_read_header/data for TNO-specific gTec MATLAB format
• 1560 - clean up file extensions in realtime/bin directory
• 1574 - baseline/normalization with grand averaging
• 1577 - ft_volumelookup adds fields which are forbidden
• 1594 - consider whether spm_bwlabel should also be in default fieldtrip
• 1629 - ft_databrowser: implement right-click context menu for 'selfun'
• 1633 - ft_databrowser: preproc-window
• 1641 - ft_databrowser: implement magical mouse-wheel-scrolling
• 1642 - ft_databrowser: implement even more magical data-dragging
• 1686 - improve debugging of end-users problems using logging options
• 1691 - ft_multiplotER interactive callback ignores common masked region
• 1711 - implement cfg.verbose option, together with ft_default.verbose
• 1716 - ft_artifact_zvalue x-axis can show time rather than samples
• 1728 - reorganize the ft_datatype documentation
• 1739 - ft_specest_mtmfft: rework description and implementation of angletransform
• 1767 - Improve the documentation on filtering
• 1792 - implement the realtime head localiser for the Elekta neuromag system
• 1815 - ft_prepare_mesh should make hexahedral mesh
• 1816 - extend ft_volumesegment with FSL BET and FAST
• 1817 - ft_prepare_sourcemodel should deal with input/output for simbio headmodel
• 1819 - ft_read_headshape should return the label for tetgen files
• 1867 - enhancement to reading events from neuromag data
• 1887 - extend ft_connectivityanalysis with measures for time-domain and component data
• 1891 - it would be nice if qsubcellfun could evaluate private private functions
• 1907 - automatically test the tutorials from the wiki
• 1915 - HERMES: connectivity analysis software
• 1924 - implement the deymed EEG file format
• 1938 - some small improvements to ft_analysispipeline
• 1981 - consider implementing a cheby2 filter in ft_preproc_xxxfilter
• 1991 - use callbacks in sourceplot
• 1996 - allow atlas lookup for slice viewmode in ft_sourceplot
• 2007 - Proposed changes to ft_inverse_beamformer_dics
• 2016 - Choosing lambda in lcmv
• 2020 - improve mne2grad - sample the leadfield on more points and integrate over them
• 2026 - Suggestion for MRI and MEG coregistration (particularly useful for neuromag users)
• 2043 - ft_connectivityplot missing cfg option
• 2047 - make spike preamble and postamble consistent with rest of FieldTrip
• 2074 - ft_spike_plot_raster: trial selection results in sparse raster plot
• 2090 - ft_rejectvisual holds the command-line while browsing trials/channels/summary
• 2112 - have ft_prepare_neighbours accept electrode file as template
• 2145 - explain options surfplot
• 2152 - ft_rejectvisual: also return trlsel
• 2184 - settle on convention for upper/lower case method names
• 2185 - enhancement: keep time dimension in ft_sourcegrandaverage.
• 2188 - enhancement: implement support for Localite marker positions (eeg-electrodes and tms-coil location)
• 2194 - enhancement: allow ft_databrowser to mark entire trial as artifact with single keystroke
• 2200 - explain on page 1 how to get support
• 2283 - ft_connectivityplot needs a legend in case of multiple inputs
• 2287 - implement tfce
• 2309 - Java Buffer Client : bug fix for freeze when buffer disconnects unexpectedly
• 2331 - ft_channelrepair should update grad.tra
• 2348 - ft_databrowser channel identify in vertical mode
• 2362 - cfg.toi in ft_freqanalysis
• 2385 - create 3D easycap elec-files
• 2386 - plot electrodes as disks in ft_plot_sens
• 2388 - consider adding support for cytoarchitectonic atlas
• 2390 - implement support for the XDF data format
• 2406 - ft_channelrepair should have method=average
• 2422 - pos2dim3d needs the statistics toolbox for a simple zscore
• 2423 - Bug Johanna with a bug
• 2424 - ft_prepare_layout from sens rather than from elec/grad
• 2425 - ft_datatype_sens fails on montaged grads
• 2428 - wilson2x2 complains about unequal frequency axis with foilim = [0 Ny]
• 2430 - add support for LSF backend
• 2431 - mpi_customized_acticap64 layout can be improved
• 2433 - bugzilla sets default severity to 'enhancement'
• 2437 - consider using image opening to post-process thresholded map when doing (source) statistics
• 2454 - Allow 'zeromax' and 'minzero' for cfg.zlim in ft_topoplotTFR and ft_singleplotTFR
• 2470 - Allow freq statistics over custom fields
• 2490 - implement support for synchronizing MEG data with video and/or audio recordings
• 2496 - change order of isolines and surface plotting in ft_plot_topo
• 2574 - ft_plot_topo: added imagesc+saturation for saving nicely vectorized topo's
• 2577 - improve the svn log messages for autosync updates
• 2582 - improve support for ft_realtime_micromedproxy
• 2601 - allow user specification of where qsubcellfun maintains it input/output files
• 2607 - Display HOSTNAME in qsubget
• 2630 - implement ft_globalmeanfieldpower
• 2638 - consider adding a microdonation service to the fieldtrip wiki
• 2672 - Neuromag EEG layout for distribution / documentation
• 2686 - make a tutorial using 4D/BTi data
• 2687 - fontsize in ft_multiplotER
• 2691 - ICA plotting in databrowser: button "component" instead of "channel"
• 2710 - enhancement for ft_databrowser 'next segment' button
• 2724 - ft_multiplotXX printing in landscape mode should be option, not default
• 2748 - Redundant or unnecessary work in ft_sourceanalysis
• 2767 - improve support for averaged neuroscan fif files
• 2793 - add mini version of spm12 to fieldtrip/external
• 2794 - implement support for the KRISSMEG data format
• 2801 - calling ft_stratify gives error when too many Curve Fitting Toolbox licenses are used
• 2813 - ft_statfun_diff_itc doesn't create/output a critval
• 2815 - ft_warp_apply has missing from its documentation the options 'sn2individual' and 'individual2sn'
• 2872 - implement support for Jinga-Hi JAGA16 system
• 2885 - collect video material from 2015 Nijmegen MEG toolkit
• 2892 - add support in ft_analysispipeline for Tim's Pipeline Program
• 2903 - replace the FT findcluster function with the refactored version from LIMO
• 2918 - support reading and writing of BrainVision BVEF electrode position files
• 2951 - implement lagged coherence in ft_connectivityanalysis
• 2955 - implement saturation option in ft_plot_mesh
• 2960 - adding ft_plot_patch.m
• 2980 - possible speed increase: allow ft_plot_XXX functions to work with vpos being a vector (instead of only scalar)
• 3004 - making cfg.trialdef.eventtype = '?' the default
• 3019 - error using fieldtrip functions in a gui.
• 3032 - add "restore all" button to GUI for ft_rejectvisual in summary mode
• 3083 - ft_connectivitysimulation should have a cfg.randomseed option
• 3092 - recognize label and unit size for micromed data
• 3161 - Add support for cross-spectrum to ft_freqdescriptives
• 3168 - Include Maxfilter functionality
• 3183 - cfg.outputfile saves default variable names that are difficult to guess
• 3253 - Integrate TSSS toolbox and SSS-beamformer in FT
• 3254 - ft_sourceplot does not initialise ft_progress based on cfg.feedback
• 3300 - Plot negativity upwards
• 3306 - implement an interface for the openbci gangion board
• 3316 - add sampling rate information to artifact structures
• 3325 - Proposed enhancement to coloring of sensors/electrodes in ft_plot_sens
• 3339 - it would be nice if trialinfo could be a table rather than a numeric array
• 3354 - sampleinfo should be updated after using ft_selectdata to make a latency selection on raw or timelocked data.
• 3380 - MOCD - mother of all Chinese documentation bugs
• 3385 - implement support for GSR/EDA data
• 3450 - DBS artifact removal functionality
• 3451 - DBS artifact removal functionality
• 3456 - Oblique way of dealing with trial-definition in ft_appendspike