Merge branch 'spm:main' into main

Author: Y-Bezs

Diff for: docs/development/git.md

@@ -27,34 +27,6 @@ During installation, you can accept most defaults. There are three options to be
 ![line ending conversions](../assets/figures/git_windows_eol.png){ width="45%" }
 ![default behavior of `git pull`](../assets/figures/git_windows_rebase.png){ width="45%" }
 
-If you do not have the administrative permissions to install Git as described above, try and install [64-bit Git for Windows Portable](https://git-scm.com/download/win) to `C:\wtcnapps\` and add the directory containing `git.exe` to the `Path` environment variable for your account.
-
-<!--
-TortoiseGit is another graphical interface for Git on Windows:
-
-* [TortoiseGit](https://tortoisegit.org/)
--->
-
-<!--
-
-It is also recommended to install the Visual Studio Code text editor and WinMerge:
-
-* [Visual Studio Code](https://code.visualstudio.com/)
-* [WinMerge](https://winmerge.org/)
-
-### Visual Studio Code Extensions
-
-Visual Studio Code has a native support of Git:
-
-* [Git Support in Visual Studio Code](https://code.visualstudio.com/docs/editor/versioncontrol#_git-support)
-
-but some extra extensions are worth considering for MATLAB development:
-
-* [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker)
-* [MATLAB](https://marketplace.visualstudio.com/items?itemName=Gimly81.matlab)
-* [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh)
-
--->
 
 ## Git Configuration
 
@@ -115,8 +87,6 @@ Pull with rebase will fail if you have unstaged changes. One way around this if
 git config --global rebase.autoStash true
 ```
 
-This is equivalent to using `git fetch` followed by `git rebase --autostash` (or `git stash`, `git pull`, `git stash pop`).
-
 As before, to apply this setting from GitHub Desktop, you need to open the command prompt by selecting ++"Repository"++ then ++"Open in Command Prompt"++ from the top menu and enter the above command line.
 
 ## Clone the SPM repository

Diff for: docs/tutorials/opm/formats/index.md

@@ -52,6 +52,30 @@ S.positions = 'positions.tsv';
 D =spm_opm_create(S);
 ```
 
+## MAG4Health 
+MAG4Health also uses the existing  `.fif` format  and can take advantage of existing fileio available in SPM.
+
+```matlab
+S = [];
+S.data = 'raw.fif';
+D =spm_opm_create(S);
+```
+
+The channel types may not be listed correctly in the file. If so we can manually set the channel type with SPM. This sets all channels to the type `MEGMAG`
+
+```matlab
+D = chantype(D,1:size(D,1),'MEGMAG');
+D.save();
+```
+
+Currently, the second tangential axis of these sensors has a higher noise floor than the other 2. We can identify and mark these channels as bad using he following code. 
+
+```matlab
+badinds = D.selectchannels('regexp_(.*tang2$)');
+D = badchannels(D,[badinds],1);
+D.save();
+```
+
 ## Neuro-1
 The Neuro-1 system developed by QuSpin currently records data in `.lvm` files. just as with the other data files we can provide additional metadata in the form of `.tsv` and .json files