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Cartool Releases

You can see here the changelog of the various releases of Cartool, to access the Download of Cartool itself, it's here.

Cartool 5103 (Christmas Edition)

posted Dec 12, 2017, 5:42 AM by Cartool Software FBMLab   [ updated Dec 12, 2017, 5:46 AM ]


What's new:

  • Memory issues:
    • Found a way to increase the possible memory load of Cartool.
    • Also the RIS Computation toolbox has been revamped to be able to deal with multiple conditions at once with Resting States dataset.
  • Computing RIS files & Standardization:
    • Z-Score factors are now estimated through multiple resampling of the data
    • Also using more robust stats, to be less sensitive to artifacts
  • Bad Epochs detection !NEW!:
    • First version (tested but not finished) of a utility to help detect the bad epochs on EEG or RIS tracks.
    • Called from menu  Markers | Scanning for Bad Epochs
    • Basically flagging maps which electrodes have clearly a non-Gaussian distribution.
    • User can launch the automatic detection and specify a tolerance factor. It is recommended to then review the results to remove any possible overzealous flagging.
  • Segmentation:
    • If the  Bad Epochs  field is selected but left empty, then Cartool will use the new automatic detection (see above) to guess where the bad epochs are.
    • User can now Drag&Drop a complete directory, all the track files within it will be added as a new group.
  • Tracks Interpolation: a few fixes.


Cartool 5000 Automn 2017 Edition

posted Oct 9, 2017, 9:50 AM by Cartool Software FBMLab

This is the 2017-10-09 edition.

What's new:

  • !New! MRIs Preprocessing toolbox:
    • Totally rewrote the old MRIs Preprocessing interface, now with a proper GUI and additional features!
    • A Presets list for the most common preprocessing cases, f.ex. before the creating Inverse Matrices.
    • It can now downsampling by targetting a given voxel size, f.ex. 1[mm]., or a given downsampling ratio.
    • Axis reorientation, to end up in a preferred orientation like the MNI space, or any other referential.
    • Sagittal Plane adjustment, so that the brain perfectly is as symmetrical as possible on the left-right axis.
    • MNI Transverse Plane adjustment, so that the brain transverse planes are in a well known referential.
    • Setting the MNI center, near AC, or setting a geometrical center.
    • Optionally doing the Skull Stripping, with a choice among 2 methods. Then applying the Bias Field Correction.
    • Current File Processing of Batch File Processing modes available.
    • Reference Guide has been written for this new toolbox.
  • Inverse Matrix Creation:
    • Solution Points can now optionally cover the whole brain, instead of the grey matter alone.
      This is often useful for brains like newborns, or for animals, for which the grey matter extraction might fail.
    • Slight improvement of the 3 Shells Lead Field model.
    • Improved the responsiveness of the Electrodes Coregistration.
    • Many fixes...
  • Toolbox to Compute Results of Inverse Solutions:
    • Updated the Reference Guide.
  • PCA Computation:
    • Toolbox to compute a robust PCA for EEG tracks. The main effort being on the robustness (Mahalanobis Covariance).
    • PCA can also be computed on the topographies alone, data being normalized beforehand.
    • ICA is a work in progress...
  • Plus many fixes (display, BrainVision files, Analyze files...)



Cartool 4856 Summertime 2017 edition

posted Oct 9, 2017, 9:16 AM by Cartool Software FBMLab   [ updated Oct 9, 2017, 9:21 AM ]

The june 2017 edition.

What's new:

  • Inverse Matrix Creation:
    • Added an Age input, to adjust some parameters according to the demography of the inverse:
      • the skull thickness
      • the skull relative conductivity
    • Skull estimate from the T1 has been greatly improved
    • Lead Field precision has also been improved
    • User can now officially use a Grey Mask as input, instead of a full brain
    • Tons of fixes...
  • !New! toolbox to Compute Results of Inverse Solutions:
    • Tools | Inverse Solutions | Computing RIS now launches a dialog to setup the most appropriate parameters to compute the RIS. It replaces all other pre-existing means & toolboxes.
    • It does extensive tests across all the input files to check their global constistency & compatibility
    • Presets option is used to quickly set the parameters for either ERPs, Spontaneous or Frequency data.
    • Results type can be the Norm of dipoles (recommended), or the dipoles as vectors.
    • Regularization can be Automatic (recommended), or fixed.
    • Z-Score can (should) be applied on the results, to account for the variation in powers across solution points.
    • ROIs can then be applied, which helps reducing the output size.
    • In case of Grouped conditions for EEG, Cartool offers to compute the average of each final group (how nice)
    • Finally, it offers to output the results as volumes (Analyze format), for a more fMRI flair.
    • Basic use:
      • 1 Inverse Matrix
      • 1 or more EEG / Frequency files, grouped by conditions (similar to Fitting f.ex.)
      • 1 XYZ file for Spatial Filtering
      • Z-Score results
    • Advanced uses:
      • Give it Frequency files to compute the RIS per frequency
      • Applying ROIs to shrink the results
      • Saving as volumes
  • Export Tracks:
    • You can append null tracks(s) while exporting
    • There was a bug, when sometimes the triggers / markers were not exported
  • Tracks Interpolation:
    • Major internal rewrite & fixes
    • Copied markers could sometimes be erroneous


Cartool 4698 Springtime 2017 edition

posted May 3, 2017, 3:28 AM by Cartool Software FBMLab   [ updated Oct 9, 2017, 9:19 AM ]

This is the latest edition of Cartool, with a lot of changes in the micro-states segmentation, inverse matrices computation, etc...


What's new (long):

  • Optimally tuned Meta-Criterion for clustering:
    • Through extensive tests with synthetic data, the optimal clustering criteria have been selected (7 of them).
    • An optimal merging formula has also been devised, to produce a single synthetic Meta-Criterion.
    • Meta-Criterion works for ERPs, Resting States, either on individual or group analysis.
  • Segmentation in Inverse Space:
    • Introduced since awhile, the method has been improved and refined. Basically, it's the clustering just done in the Inverse Space instead of the EEG space.
    • For ERPs, RIS templates can be anything they want. But for Resting States, RIS templates are now forced to be non-overlapping, like independent regions.
    • It extracts both the clustering and the localization in the same process! It has been tested extensively on a lot of datasets, and produces consistent results.
  • Segmentation with a dual dataset !NEW!:
    • Within the EEG RS analysis, Cartool can now compute the corresponding RIS templates from the EEG templates. This allows to see what were the sources associated with all the EEG maps clustered together.
    • Conversely, it can compute the corresponding EEG templates from the RIS templates. This time it allows to see the EEG maps associated with all the Inverse data clustered together.
    • This is the optimal way to have the correspondance between the EEG and the Inverse Space templates.
  • Fitting will output more correlation data: the spatial correlation time courses, but also some cross-correlations of these time courses.
  • Frequency Analysis:
    • Frequency Analysis in the Inverse Space !NEW!:
      • Perform first the frequency analysis on the EEG, saving the results to Complex values.
      • Cartool can now apply the Inverse Matrix to these Complex data to obtain the resulting sources (Tools | Inverse | Computing RIS). This is done by applying the Real and Imaginary parts separately, then merging the results together.
    • You can now save the Phase from the wavelet analysis (S-Transform).
  • Correlation analysis:
    • 3 types of analysis are now available:
      Spatial Correlation; Time-course Correlation; Phase-Intensity Coupling.
      Most of these analysis can be done on tracks or on frequencies, with Cartool performing a lot of checks on the given data.
    • Spatial Correlation:
      • Given some EEG (or RIS) files, and some templates, computes the instantaneous spatial correlation with each template. This is the same as in the Fitting.
      • Results are time courses of these correlations.
    • Time-course correlation:
      • Given some time courses (whatever they are), compute the correlation between them. F.ex. to see the correspondance between templates spatial correlation and the solution points.
      • Result is a matrix of correlations.
    • Phase-Intensity Coupling !NEW!:
      • Given some phase and intensity files, computes the coupling between the two.
      • Result is a frequency file, showing the coupling for a given ROI / track with all the others.
  • Generating synthetic data for various tests, called from menu  Tools|Generating Synthetic Data:
    • There are currently 3 ways to generate data: EEG segments, RIS segments or dipole sources.
    • From a given number of core EEG maps, you can generate synthetic EEG segments. Correlation, noise levels and segments durations are controlled by the user.
    • Likewise in the Inverse Space, generating artificial inverse segmented data.
    • Any  number of oscillating dipoles, each with its own location, orientation, amplitude, frequency and phase. Results are given in both the EEG and Inverse spaces.
  • Inverse Display: you can now select the solution points and it will show up in the RIS tracks, or select some RIS tracks and it will show up in the inverse solution points. This is similar to the maps display, where you can select the electrodes.
  • Other stuff:
    • Utility to split freq files in any of its dimensions: per frequency, per eelctrode or per spectrum.
    • Refreshed the MRIs | Preprocessing utility. You can now explicitly reorient, downsample, coregister, extract brain + Bias Field correct.
    • Improved the topographic PCA, to be working in both EEG and RIS spaces.
    • Reading Analyze files with exotic formats, like float / doubles with possible NaN values...
    • Fixing old bugs (..and introducing new ones for the LOLs).


Cartool 3.52 (2847)

posted Oct 22, 2012, 10:24 AM by Cartool Software FBMLab   [ updated Oct 22, 2012, 10:25 AM ]

A maintenance release.

Inverse Solutions

  • Inverse display: switched back to the 4 Nearest Neighbors (4NN) instead of previously 1NN ("constant cubes"). Display looks better, and is fast enough.

  • Exporting results as volume: remains with 1NN for the moment, which means constant values in "cubes" around each solution points. Advantage being: no interpolation nor extrapolation, just the raw values ready for your own processing.

  • Better color palettes, plus 2 more: one contrasty black to yellow, and one which gives annular-like results.

  • Improved the display quality of the inverse itself when doing snapshots.

  • Solution Points: better detection of minimum distance across all points.

Other stuff

  • BrainVision files, reading format 2.0.

  • Many bugs fixed, too long to list (and to read?).


Cartool 3.52 (2693)

posted Oct 22, 2012, 10:09 AM by Cartool Software FBMLab   [ updated Oct 22, 2012, 10:25 AM ]

I am currently working on the new Spindle Detection feature. In the mean time, I upgraded & fixed many things:

  • Export Tracks
    Fixing some glitches.

  • Tracks Display
    Upgraded the Markers functionnalities.
    Bug when opening a content with positive data, the average reference could kick in (which it shouldn't).

  • EGI MFF format
    Updated to the latest format.

Cartool 3.52 (2500)

posted Feb 13, 2012, 10:33 AM by Cartool Software FBMLab   [ updated Feb 13, 2012, 10:33 AM ]

This version aims at tightening a bit the bolts, and should run much better for memory intensive processing.

Improvements

  • Scanning Markers boost: now it runs much, much faster (about 100x), even with filters on.

  • Export Tracks boost:
    • Speed dramatically improved, especially when using some filters (about 25x)!
    • Fixing some rare glitches, like wrong GFP in case of Baseline Correction, or wrong Average in case of re-referencing or rescaling.

  • Creating ROIs dialog:
    • There are now 2 lists of names the user can provide:
      • One is a kind of dictionary of the indexes found in the Mask volume;
      • The other one is the list of ROIs you actually want as output.
    • There is now a specific option for the AAL mask, its labels being directly encoded within Cartool.
    • An output ROI can merge multiple input ROIs together.
      (See the Help to get more details)
    • A few bug fixes, like with the center of the MNI template...

  • Statistics: made some internal changes to run with less memory, especially in case of .ris analysis!
  • Made many optimization regarding the memory use.
  • EEG Filters: some speed improvement.
  • MRI display now have a specific Histogram sub-menu, from the Filters menu.


Bugs

  • S-Transform in Frequency Analysis: the 0Hz output (average of the signal) could be outputted signed, even when saving the Norm or Norm2 of the signal!
  • Many little bugs won't see the end of winter...


Cartool 3.51 (2453)

posted Jan 24, 2012, 3:08 AM by Cartool Software FBMLab   [ updated Jan 24, 2012, 3:08 AM ]

Fixing the Brain segmentation (CSF / Grey / White matters) and improving the Bias Field Correction.

New features

  • Use a Mixture of Gaussians to compute the CSF / Grey / White matters level. Using these new levels to compute the grey segmentation more accurately.
  • Semi-transparent cursors, in tracks and frequencies display, for a less retina-destroying experience!
  • Added a Histogram menu in the Volume (MRI) filters:
    • Computing histogram,
    • Equalization,
    • Compaction (reverting equalization).
  • Improved the Bias Field Correction to behave better near the edges of the brain.

Bug fixes

  • Export tracks: many minor glitches fixed (exporting triggers, correctly reverting filters, tracks specification...).
  • Grey segmentation improved / fixed with the new Mixture of Gaussians.
  • Solution Points computation (Inverse Solutions) tuning.

Cartool 3.51 (2381)

posted Dec 12, 2011, 5:48 AM by Cartool Software FBMLab   [ updated Dec 12, 2011, 5:48 AM ]

A few bug fixes and new features.


Bug fixes

  • Creating Inverse Matrices: in some rare case (very high bias field near the neck), 'Gluing' the electrodes while coregistering the electrodes on the MRI could fail near the neck.
  • Electrodes files (.xyz or .els) orientation detection could fail in some rare case, when some of the 10-10 system electrodes were missing.

New features

  • EEG: a set of  3 Tracks Analysis tools (called from the  Selection|Tracks Analysis  menu), can help sorting out which tracks are flat, broken, noisy, or all at once.
    The aim is to detect useless tracks for an averaging. See the Help for more details...
  • EEG display: restored the ability to rescale some tracks individually.
    First select the targetted tracks (middle button as usual), then use Control + Shift + right click  (instead of Shift + right click).
  • MFF files: now you can Drag & Drop the MFF directory directly into any of the Cartool dialogs, Cartool will translate the directory into its corresponding signalXX.bin  files.
  • EEG display: revamped the Trigger/Marker display with darker text colors for better readability, and lighter colors in the body filling for better visibility.
  • EEG display: revamped the  Selection  menu with clearer description, organization, and a few more functions.

Cartool 3.51 (2345)

posted Nov 24, 2011, 9:03 AM by Cartool Software FBMLab   [ updated Nov 24, 2011, 9:03 AM ]

Mainly, this version is about reading the new EGI file format "MFF". There are quite some bug fixed, too...


Note: it is highly recommended to really restart your machine after you installed this version, as the Windows file association/icons have been changed (in plain english, which file has which icon).


MFF files

  • Files are store in a directory structure (package for Mac), which holds a lot of descriptive files something.xml and the data signalXX.bin (XX being a number).
    Don't delete, modify or rename any of these files, or you will break the coherence of this structure!
  • To open a MFF file in Cartool, simply use the signalXX.bin file.
    Another very convenient way to do is to Drag&Drop the directory structure itself in Cartool, which will open all the signal files it contains.
  • Triggers from the DIN input are simply coded with their values (as usual), like "123".
  • Triggers from the MultiPort ECI input are coded like "code:name":
    • code being the category of the trigger,
    • name being either the description, the label, or nothing if both are missing.
  • Multiport ECI triggers can also have keys, in which case Cartool add a trigger at the same position with a name "key=data".

Bug fixes

  • Normalizing MRIs: non-integer voxel sizes would lead to anisotropic voxels; origin could be wrongly set; size could be too small sometimes.
  • Big vectorized-types BrainVision files were very slow.
  • EGI .nsr files: triggers are now shown like "code:name", code being a category set by the stimulation program, and name the actual trigger; fixed reading some types of triggers (DIN with 255 values).
  • Switching to another EEG session/sequence now preserves (most of) the state of the window, like the bad channels, display type, etc...
  • Tracks display now has enough space for the channels' name.


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