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version_info
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ALICE
version 8.2
Date: 12 December 2023
Author: Mariana P Branco ([email protected])
Place: UMC Utrecht
--------- Info log: -----------------------------------------------------------
[ v8.2 14-12-2023 ]
_____Bug fix/improvements_______________________________________________________
+ When HD is acquired in same file as clinical grids, there was an error for neuralact,
due to nan in the channel list. This has been corrected.
+ Remove the pre-selected hemisphere when a new layout is created.
--------- Info log: -----------------------------------------------------------
[ v8.1 11-09-2023 ]
_____Bug fix/improvements_______________________________________________________
+ Added the original path of CT/MRI/FS files to the log files.
--------- Info log: -----------------------------------------------------------
[ v8.0 27-01-2023 ]
_____Bug fix/improvements_______________________________________________________
+ correct bug when selecting grids/shafts with similar names (e.g. TOL and OL).
Using ismember() instead of contain() to find the whole label string instead of parts of string.
--------- Info log: -----------------------------------------------------------
[ v7.9 07-09-2022 ]
_____Bug fix/improvements_______________________________________________________
Note: many of the improvements and new features were suggestions from Julia Berezutskaya, as she uses ALICE the most.
She suggested to move from channel indices to channel labels, and was agreed in the group.
+ selects cluster using labels. the indices inside electrode_CM.1D are indices of the labels file.
+ remove the grid settings 'indices'. electrodes are identified from labels file.
+ runHermes, runHD and runsEEG were adjusted to read labels and save labels in txt/tsv output
+ added permissions to folder recursively via the terminal (unix) because sometimes some files were not sorrectly.
+ ALICE version added to log files
+ added errordialog for when electrode labels are not input before electrode selection or visualization or for previous versions.
When running new ALICE with old output folder, the user needs to input a electrode_label txt file.
+ for each tab there is a hemisphere and method attached.
+ added option to interpolate sEEG electrodes when selecting only 1st and last in shaft.
--------- Info log: -----------------------------------------------------------
[ v7.8 05-05-2021 ]
_____Bug fix___________________________________________________________________
+ it can now delete the grid select and not just the last one
+ grid settings add to the text entry on the interface are now separated by ; instead of
, to avoid confusion with electrodes sleected inside [ ].
+ fix bug of disabled previousGrid button when moving forward on the grids list
--------- Info log: -----------------------------------------------------------
[ v7.7 09-11-2020 ]
_____Bug fix___________________________________________________________________
+ added ; after disp in alice.m
[ v7.6 03-11-2020 ]
_____Bug fix___________________________________________________________________
+ remove error when trying to close ALICE without creating/locating directory
[ v7.5 02-11-2020 ]
_____Bug fix___________________________________________________________________
+ enable tabs when 'locate directory' with layout empty.
[ v7.4 19-09-2020 ]
_____Bug fix___________________________________________________________________
+ set varargin parameter in ctmr_gauss_plot for 'facealpha'.
+ fix NAN label for empty channels in funciton runXXX.m
[ v7.3 10-09-2020 ]
_____Bug fix___________________________________________________________________
+ set permissions to ALICE folder when closing ALICE. Do cd('ALICE') before setting permissions
+ fix indexing of HD grid electrodes in projection script.
+ loading tabs: delete tabs before settings them ups
+ runHD.m: added code to put nan in elecmatrix after loading coordinate files.
[ v7.2 07-09-2020]
_____Bug fix___________________________________________________________________
+ locate directory button didn't load empty layout tab/paths
[ V7.1 27-07-2020]
_____Bug fix___________________________________________________________________
+ defined layout as empty cell with 3 entries. fixed bug when swaping between layouts.
_____Minor update______________________________________________________________
+ added information in documentation about layouts (version 21-07-2020).
[ v7 21-05-2020 ]
_____Major updates_____________________________________________________________
+ added option to project in both hemispheres simultaneously.
+ added option to project in two hemispheres one after the other using new set of grids.
+ when projecting two hemisphere, results are combined in results folder and not deleted.
--> several functions and files have now hemisphere on the name/input.
+ creates txt file in step 3 with coordinates and labels of electrodes for all methods.
--> only works for matlab version more recent than (and including) 2019a.
+ changed grid settings input in step 3: allows for (max) 3 layouts (using tabs) and to navigate between grids/tabs.
+ output directories changed, now: /results > method > hemisphere > intermidiate_results & /pictures/.
____Minor updates______________________________________________________________
+ added checkbox for saving nifti files of projected electrodes.
- removed single grid .*img files.
+ substitute img/hdr by .*nii files.
+ implemented facealpha as argument of ctmr_gauss_plot and subsequent functions.
+ added nifti output of projected electrodes for sEEG method.
+ added error when the located folder is not called ALICE.
+ cleaned up of electrodes clusters not in the grid specs.
+ allows choice of hemisphere and grid settings for HD method.
+ added waiting bar when plotting the brains and pause between saveas functions.
+ corrected the error when locating directory of copied folder. now opens in new directory.
- removed value 9 from help message dialog displayed after CT is aligned to MRI.
+ added -niml -yesplugouts to afni call in alignCTtoT1_shft_res.csh
- removed Settings structure from alice.m.
+ enlarged width of main window by 10 points.
- remove computation of balloon for HD method (not required).
+ save settings.mat after runing the projection methods and after each layout.