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Automatic EEG localization and labelling using Revopoint 3D #716

Merged
merged 186 commits into from
Nov 6, 2024
Merged

Automatic EEG localization and labelling using Revopoint 3D #716

merged 186 commits into from
Nov 6, 2024

Commits on Jun 28, 2024

  1. initial commit: enable importing wavefront obj files into brainstorm

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Commits on Jul 13, 2024

  1. refactoring: add input checks, remove unwanted code

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Commits on Jul 15, 2024

  1. add 'Color' field to the surfacemat structure templates

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  2. add check for 'Color' field

    @chinmaychinara91
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  3. Update menu: 'Digitizer' and 'Revopoint' under the bracket 'Digitize'

    @chinmaychinara91
    chinmaychinara91 committed Jul 15, 2024
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  4. Refactor 'panel_digitize' to add conditions for 'Revopoint'

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    chinmaychinara91 committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. support visualizing per vertex color for imported OBJ mesh in BST

    @chinmaychinara91
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  2. continued: enable importing wavefront obj files into brainstorm

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  3. External added: Piotr Image and Video Toolbox (https://github.com/pdo… 

    …llar/toolbox)

required for warping and interpolating points on EEG cap
    @chinmaychinara91
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  4. deface a 3D mesh

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Commits on Jul 17, 2024

  1. Tag imported mesh with color as 'textured'

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  2. Handle displaying a 'textured' mesh

    @chinmaychinara91
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  3. Key 'c' as shortcut for collecting points from Revopoint mesh

    @chinmaychinara91
    chinmaychinara91 committed Jul 17, 2024
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  4. Refactor importing wafefront obj 

    - it is always going to be a meshed OBJ so 'FileType' parameter is unnecessary
- renamed 'tri' as 'faces'
- renamed 'pos' as 'vertices'
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Commits on Jul 18, 2024

  1. handle mesh without texture information

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    chinmaychinara91 committed Jul 18, 2024
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  2. Update comment

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  3. intial commit: automatic detection and labelling of EEG cap electrodes

    @chinmaychinara91
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  4. custom layout EEG caps 

    - ANT 65 is a modeifed version of ANT Waveguard 64
- Acticap 66 is a modified version of Acticap 65
    @chinmaychinara91
    chinmaychinara91 committed Jul 18, 2024
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  5. configure 'Edit Settings' options for Revopoint

    @chinmaychinara91
    chinmaychinara91 committed Jul 18, 2024
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  6. Option to generate 100 random headpoints 

    to be used for registration to MRI
    @chinmaychinara91
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  7. fix typo bugs introduced in 3066842

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  8. 'AddMontage' function modified to handle adding Channel File as montage

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    chinmaychinara91 committed Jul 18, 2024
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  9. WIP: Handle ANT Waveguard 65 and Acticap 66 EEG caps 

    Needs work on a more generic approach to handle different EEG caps
    @chinmaychinara91
    chinmaychinara91 committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. updated comment (file description)

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  2. updated cap type

    @chinmaychinara91
    chinmaychinara91 committed Jul 19, 2024
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  3. typo in file name

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    chinmaychinara91 committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. Update Color for 'textured' mesh when downsized/downsampled

    @chinmaychinara91
    chinmaychinara91 committed Jul 22, 2024
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  2. Update comments on ways to add montage

    @chinmaychinara91
    chinmaychinara91 committed Jul 22, 2024
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  3. Update panel_digitize.m 

    - Limit display of 'Auto' and 'Random' buttons for Revopoint only
- Correct display order of EEG labels based on the initialization labels required as per the EEG cap
- Removed unwanted code for sketch points (was used for debugging)
- Creating montages from EEG cap layout mat files (only for Revopoint)
    @chinmaychinara91
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  4. load the latest (last updated) mesh to work on

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    chinmaychinara91 committed Jul 22, 2024
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  5. add to 1b3e2c8

    @chinmaychinara91
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  6. adding montage from text files only available for Polhemus

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    chinmaychinara91 committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. better handling of saving ChannelFile info to DigitizeOptions

    @chinmaychinara91
    chinmaychinara91 committed Jul 23, 2024
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  2. removing 'Color' fields from template 

    To be added only when needed
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  3. 'Color' field added to surface when needed

    @chinmaychinara91
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  4. remove commented code

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Commits on Jul 24, 2024

  1. Handle updating surface color for 'Views' menu option on 3D figure

    @chinmaychinara91
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Commits on Jul 29, 2024

  1. making sure old naming in UI is intact for 'Digitize'

    @chinmaychinara91
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Commits on Aug 1, 2024

  1. handle 'Edit Settings' for Revopoint

    @chinmaychinara91
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  2. mask unwanted menu items for Revopoint

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Commits on Aug 12, 2024

  1. 'DelimitedTextImportOptions' support for R2016b to R2018a

    @chinmaychinara91
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  2. code cleanup and reduce ambiguity

    @chinmaychinara91
    chinmaychinara91 committed Aug 12, 2024
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  3. ignore 'rmoutliers' step for < R2018b

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Commits on Aug 15, 2024

  1. remove default menu size 12 for EEG cap montages

    @chinmaychinara91
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Commits on Aug 19, 2024

  1. Merge remote-tracking branch 'upstream/master' into bst-revopoint-dig… 

    …itizer
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Commits on Aug 20, 2024

  1. support new panel calls in the legacy panel; some code cleanup

    @chinmaychinara91
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  2. adding revopoint changes to the new panel (1) and its dependencies

    @chinmaychinara91
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  3. manual point collection in new panel for revopoint

    @chinmaychinara91
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  4. new panel: collecting 100 random head points

    @chinmaychinara91
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Commits on Aug 21, 2024

  1. legacy panel: reverting adding montage from text files

    @chinmaychinara91
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  2. legacy panel: refactor montage selection in menu for Revopoint

    @chinmaychinara91
    chinmaychinara91 committed Aug 21, 2024
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  3. new panel: montage menu refactoring for Revopoint

    @chinmaychinara91
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  4. new panel: revopoint automation for detecting and labeling electrodes

    @chinmaychinara91
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  5. new panel: refactor 'Edit_Settings' menu to handle Revopoint options

    @chinmaychinara91
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Commits on Aug 28, 2024

  1. new panel: allow updating a specific EEG electrode from the coordinat… 

    …e list manually
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  2. new panel: remove unused variable

    @chinmaychinara91
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  3. new panel: handle enable/disable of the 'Auto' and 'Random' buttons

    @chinmaychinara91
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  4. new panel: User warning if 'Auto' button pressed without initializati… 

    …on points
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  5. new panel: use Digitize.Type to define the mode used

    @chinmaychinara91
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  6. legacy panel: handle 'Auto' and 'Random' visibility; some code cleanup

    @chinmaychinara91
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  7. new and legacy panel: rename Revopoint to 3DScanner for better ge… 

    …neralization
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Commits on Sep 10, 2024

  1. Bugfix: support old Digitize.Options.Montages struct

    @rcassani
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  2. GUI menu name updated: '3DScaner' to '3D scanner'

    @rcassani
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  3. Bugfix: Two entries in GlobalData.Surface were created instead of one

    @rcassani
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  4. Implement rmoutliers without arguments for older Matlab versions

    @rcassani
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  5. Ignore unused output arguments

    @rcassani
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  6. Refactor to avoid unnecessary reads to db: bst_get('Subject')

    @rcassani
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  7. Gentle exit if user cancels "Import surfaces..."

    @rcassani
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  8. Clean code. Avoid copy-paste

    @rcassani
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  9. Cleaner

    @rcassani
    rcassani committed Sep 10, 2024
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Commits on Sep 11, 2024

  1. Add Color field for all surface files and loaded surfaces 

    - Avoid different versions of surfaces files and loaded surfaces
- Avoid many checks for `Color` field
    @rcassani
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  2. Treecallback for Display texture surface 

    - Right-click > Display has same behaviour as double-click
- Do not load surface on right-click, that slows the popup menu display
    @rcassani
    rcassani committed Sep 11, 2024
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  3. Bugfix typo

    @rcassani
    rcassani committed Sep 11, 2024
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  4. Avoid copy-paste same method call

    @rcassani
    rcassani committed Sep 11, 2024
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  5. Parse input in panel_digitize_2024('Start')

    @rcassani
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  6. Not apparent reason to have a different panel name

    @rcassani
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  7. Add progress bar to 'EEGAutoDetectElectrodes'

    @rcassani
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  8. Parse input in panel_digitize('Start') 

    See: 3d77e53
    @rcassani
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  9. Refactor to avoid unnecessary reads to db: bst_get('Subject') 

    See 1c2c2b0
    @rcassani
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  10. Not apparent reason to have a different panel name 

    See 8d6bc3b
    @rcassani
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  11. Code easier to read

    @rcassani
    rcassani committed Sep 11, 2024
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  12. Bugfix

    @rcassani
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  13. Remove unnecessary FOR loops

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Commits on Sep 12, 2024

  1. handle Digitize as input to DigitizerType parameter

    @chinmaychinara91
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  2. Revert "handle Digitize as input to DigitizerType parameter" 

    This reverts commit 53f43dd.
    @chinmaychinara91
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  3. Better handling of calls to Start function 

    recommended here: brainstorm-tools#716 (comment)
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Commits on Sep 13, 2024

  1. No scaling needed as OBJ vertices are unitless

    @chinmaychinara91
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  2. new panel: avoid copy pasting; add comments

    @chinmaychinara91
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  3. function to compartmentalize automatic detection and labelling

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  4. clean code; call compartmentalized function

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Commits on Sep 15, 2024

  1. legacy panel: avoid copy paste 

    sync with changes as above for the new panel
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  2. bugfix: missed some call checks

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Commits on Sep 16, 2024

  1. code cleanup; comments added

    @chinmaychinara91
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  2. avoid copy/paste for Edit settings

    @chinmaychinara91
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  3. add comments; clean code and calls auto_3dscanner

    @chinmaychinara91
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  4. changed surface description 

    avoid using 'head' keyword because if renamed having `head` word in it, the `node_rename` function converts the type to `Scalp`.
    @chinmaychinara91
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  5. remove comment; in_tess handles node naming

    @chinmaychinara91
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  6. handle textured surface import and selection

    @chinmaychinara91
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Commits on Sep 17, 2024

  1. do not delete 3D scanner figure when resetting

    @chinmaychinara91
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  2. textured surface handling: allow user to choose from options 

    The options:

1. Subject has no textured mesh or subject does not exist at all:
 - Import surface GUI pops up, user chooses the surface and it gets loaded
2. Subject already has 1 or more than 1 textured mesh in it then user is given an option:
 - Use existing - if only one mesh present then it just loads that directly; if more than one present then user is given an option to choose which one he wants to use
 - Add New - Import surface GUI pops up, user chooses the surface and it gets loaded
 - Cancel / Press (X) at any instant - cancels the process and exits
    @chinmaychinara91
    chinmaychinara91 committed Sep 17, 2024
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  3. Digitize (3D scanner) option on right click pop up for textured sur… 

    …face
    @chinmaychinara91
    chinmaychinara91 committed Sep 17, 2024
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  4. Better way to get the open surface details

    @chinmaychinara91
    chinmaychinara91 committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. make textured surface comments unique; show comments as choice to use… 

    …rs to choose from

- Unique comments for same textured mesh makes it easy for the user to distinguish one from the other
- When user clicks 'Use existing' the list of textured surface comments pop up for the users to choose from. This is more intuitive for the user than having to choose from the filename which sits in the database.
    @chinmaychinara91
    chinmaychinara91 committed Sep 18, 2024
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  2. add comments

    @chinmaychinara91
    chinmaychinara91 committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. collect 100 points without reducepatch

    @chinmaychinara91
    chinmaychinara91 committed Sep 19, 2024
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  2. bugfix: display correct label text on deleting-updating landmark coor… 

    …dinates
    @chinmaychinara91
    chinmaychinara91 committed Sep 19, 2024
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  3. Avoid copy-paste same method call

    @chinmaychinara91
    chinmaychinara91 committed Sep 19, 2024
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  4. Fixes 128c9b0

    @rcassani
    rcassani committed Sep 19, 2024
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  5. Clean code

    @chinmaychinara91
    chinmaychinara91 committed Sep 19, 2024
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  6. for Start over, close and reset figure for 3D Scanner

    @chinmaychinara91
    chinmaychinara91 committed Sep 19, 2024
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Commits on Sep 23, 2024

  1. bugfix: Right click on subject > Import surfaces

    @chinmaychinara91
    chinmaychinara91 committed Sep 23, 2024
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  2. better way to access the current surface file

    @chinmaychinara91
    chinmaychinara91 committed Sep 23, 2024
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  3. import head surface obj with units using fieldtrip's ft_convert_units

    @chinmaychinara91
    chinmaychinara91 committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. legacy: better way to access the current surface file

    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  2. update the correct caps based on the protocol

    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  3. update landmark initialization points

    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  4. add all other surface property calculations 

    required as the updated surface will be saved to database
    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  5. save the surface and update the node

    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  6. check spm12 installation for ft_convert_units 

    `ft_convert_units` is part of spm12/external/fieldtrip
    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  7. bugfix

    @chinmaychinara91
    chinmaychinara91 committed Sep 24, 2024
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  8. replace erase with strrep for backward compatibility

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    chinmaychinara91 committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. improve obj parsing (see description) 

    - updated the code reference from where this was inspired
- for some obj, obtained from 3D software like Maya and Blender, when parsed using  'readtable', the vertex coordinates start from the 3rd column
- `refine` is a FT function to improve resolution. Using this creates a processing and loading delay which can be avoided as the scans would already be in a good resolution.
    @chinmaychinara91
    chinmaychinara91 committed Sep 25, 2024
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  2. similar to ft_convert_units 

    inspired by `channel_fixunits.m`
    @chinmaychinara91
    chinmaychinara91 committed Sep 25, 2024
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  3. remove fieldtrip dependency

    @chinmaychinara91
    chinmaychinara91 committed Sep 25, 2024
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  4. typo fix

    @chinmaychinara91
    chinmaychinara91 committed Sep 25, 2024
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Commits on Oct 9, 2024

  1. generalize checking for initialization points

    @chinmaychinara91
    chinmaychinara91 committed Oct 9, 2024
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  2. adding Wearable Sensing DS-24 EEG cap layout 

    It follows the 10-20 system with 'Fpz' as GND and 'A1, A2' as  REF.
    @chinmaychinara91
    chinmaychinara91 committed Oct 9, 2024
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Commits on Oct 24, 2024

  1. Merge branch 'master' into bst-revopoint-digitizer

    @rcassani
    rcassani authored Oct 24, 2024
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Commits on Oct 25, 2024

  1. Update channel_fixunits to accept vertices 

    Remove unnecessary copies of code
    @rcassani
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  2. Simpler creation of struct (in_tess_wftobj)

    @rcassani
    rcassani committed Oct 25, 2024
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Commits on Oct 28, 2024

  1. GUI: Add feedback that surface is loading...

    @rcassani
    rcassani committed Oct 28, 2024
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  2. Simplify using already defined function handle

    @rcassani
    rcassani committed Oct 28, 2024
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  3. Simpler and meaningful variable name

    @rcassani
    rcassani committed Oct 28, 2024
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  4. Use content rather than string in filename

    @rcassani
    rcassani committed Oct 28, 2024
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  5. Cleaner diff

    @rcassani
    rcassani committed Oct 28, 2024
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  6. Unify "EditSettings" options, default values and user inputs

    @rcassani
    rcassani committed Oct 28, 2024
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  7. Correct file tag

    @rcassani
    rcassani committed Oct 28, 2024
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  8. EEG caps with landmark labels must be usable, as they allow manual loc

    @rcassani
    rcassani committed Oct 28, 2024
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  9. Add info in auto button tooltip

    @rcassani
    rcassani committed Oct 28, 2024
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  10. Enable auto button for valid caps IFF all landmarks are acquired

    @rcassani
    rcassani committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. Update function names in auto_3dscanner

    @rcassani
    rcassani committed Oct 29, 2024
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  2. Move "whiteCap" out of FindElectrodesEegCap

    @rcassani
    rcassani committed Oct 29, 2024
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  3. Bugfix: Consider that user acquires more points than landmarks

    @rcassani
    rcassani committed Oct 29, 2024
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  4. Bugfix: Setting proper tag for textured surface file

    @rcassani
    rcassani committed Oct 29, 2024
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  5. Improve warping by using all EEG points acquired by user

    @rcassani
    rcassani committed Oct 29, 2024
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  6. Remove unnecessary sorting 

    Landmarks and extra points are identified by name.
In output the locations for EEG electrodes is get also by name
    @rcassani
    rcassani committed Oct 29, 2024
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  7. Change dots in console with progress bar

    @rcassani
    rcassani committed Oct 29, 2024
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  8. Suppress expected warnings

    @rcassani
    rcassani committed Oct 29, 2024
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  9. Remove unnecessary output: auto_3dscanner('GetEegCapLandmarkLabels')

    @rcassani
    rcassani committed Oct 29, 2024
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  10. Reduce perceived lag in opening figures after fiducials are set

    @rcassani
    rcassani committed Oct 29, 2024
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  11. Unify sound of clicks across platforms for source and compiled BST

    @rcassani
    rcassani committed Oct 29, 2024
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Commits on Oct 30, 2024

  1. Avoid copy/pasting for default EEG caps menu

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  2. for <2016b: no importing WFTOBJ and 3D scanner option

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  3. rename auto_3dscanner to channel_detect_eegcap_auto

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  4. update description; expected units mm

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  5. Correct case in comments

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  6. remove unnecessary indents for cleaner diff

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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  7. bugfix: iOptionsType was not initialized; use num2str for ComPort

    @chinmaychinara91
    chinmaychinara91 committed Oct 30, 2024
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Commits on Oct 31, 2024

  1. bugfix: set global point index with found index

    @chinmaychinara91
    chinmaychinara91 committed Oct 31, 2024
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  2. Correct case in comments

    @chinmaychinara91
    chinmaychinara91 committed Oct 31, 2024
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  3. changes in panel_digitize_2024 made to panel_digitize

    @chinmaychinara91
    chinmaychinara91 committed Oct 31, 2024
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Commits on Nov 1, 2024

  1. collect random head shape points based on Brainstorm recommended way 

    https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize3dScanner#Collect_the_desired_number_of_head_shape_points
    @chinmaychinara91
    chinmaychinara91 committed Nov 1, 2024
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Commits on Nov 2, 2024

  1. explicitly mention digitize in condition

    @chinmaychinara91
    chinmaychinara91 committed Nov 2, 2024
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Commits on Nov 4, 2024

  1. revert ComPort type conversion 

    mistook it for a number
    @chinmaychinara91
    chinmaychinara91 committed Nov 4, 2024
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  2. menu_default_eegcaps: separate function for generating BST availabl… 

    …e EEG caps menu
    @chinmaychinara91
    chinmaychinara91 committed Nov 4, 2024
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  3. extend renaming of surfaces with same filename (comments) while impor… 

    …ting to all surfaces
    @chinmaychinara91
    chinmaychinara91 committed Nov 4, 2024
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  4. Add first draft of parsing of .wobj text file

    @rcassani
    rcassani committed Nov 4, 2024
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Commits on Nov 5, 2024

  1. proper columns assigned for vertices, faces and textureIdx

    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  2. use regexp to spoort older versions; only check based on Comment … 

    …for renaming
    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  3. revert back importing obj support for < R2016b

    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  4. Fix indentation

    @rcassani
    rcassani committed Nov 5, 2024
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  5. Use functions in Brainstorm to: 

    - Retrieve sSubject from MRI filename
- Generate unique comment
    @rcassani
    rcassani committed Nov 5, 2024
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  6. Bugfix: return same orientation as input

    @rcassani
    rcassani committed Nov 5, 2024
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  7. Cleaner indexing

    @rcassani
    rcassani committed Nov 5, 2024
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  8. Update regexp to handle scientific notation (using e notation)

    @rcassani
    rcassani committed Nov 5, 2024
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  9. Digitize panels, do not clear settings that are not asked to the user

    @rcassani
    rcassani committed Nov 5, 2024
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  10. Allow displaying texture surfaces with "Add surface" in surface panel

    @rcassani
    rcassani committed Nov 5, 2024
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  11. use clock instead of datetime (support older MATLAB versions)

    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  12. better way to get the surface file structure in hFig 

    tested in R2014a:  `TessInfo.hPatch` does not have the structure definitions
    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  13. supress more warnings 

    tested in R2014a: Large Radius warnings were showing up
    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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  14. add disclaimer to users that 'Auto' feature is experimental

    @chinmaychinara91
    chinmaychinara91 committed Nov 5, 2024
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Commits on Nov 6, 2024

  1. Bugfix: No check required while doing manual head shape points collec… 

    …tion
    @chinmaychinara91
    chinmaychinara91 committed Nov 6, 2024
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  2. Bugfix: Update tooltip for 'Auto' button

    @chinmaychinara91
    chinmaychinara91 committed Nov 6, 2024
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  3. Allow to cancel start of autodetection

    @rcassani
    rcassani committed Nov 6, 2024
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  4. Bugfix: Disable Auto button, when EXTRA are being acquired.

    @rcassani
    rcassani committed Nov 6, 2024
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  5. Bugfix: Wrong logic: ~cellfun(@isempty, ...) results in 1 or 0

    @rcassani
    rcassani committed Nov 6, 2024
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