BFC Playground Mac OS

Playground for PC/Mac (Version 2.5) IMPORTANT NOTE: In order to launch Playground Sessions, you need an account. Click here to Sign Up Now! Windows 7 or later (msi) Mac OS X. In the Finder search box, type Playground. Locate the Playground app, which will have an icon with a white note on a blue background and double click to open it. Once you've located Playground in your Finder, you'll then have the option of clicking and dragging it to.

• Bfc Playground Mac Os Catalina
• Bfc Playground Mac Os Download
• Bfc Playground Mac Os X
• Bfc Playground Mac Os 11

• In the Finder search box, type Playground. Locate the Playground app, which will have an icon with a white note on a blue background and double click to open it. Once you've located Playground in your Finder, you'll then have the option of clicking and dragging it to your dock, creating a shortcut for accessing it.
• Swift Playgrounds for Mac is built with Mac Catalyst, giving you the ability to edit the exact same playground file on iPad and Mac. ICloud Drive seamlessly shares your playgrounds, and changes you make on either iPad or Mac immediately appear on your other devices. It’s easy to start a project on iPad and open the file on Mac to keep coding.
• The playground makes the highly complex blockchain network easy for running. Both online and offline version of Playground is available. While the online playground runs the business network in.

Running BDP

The BDP is a command-line tool that takes diffusion images and a bias-field corrected MPRAGE image (fileprefix.bfc.nii.gz file generated by BrainSuite) as input, performs distortion correction and co-registration, and writes out the estimated diffusion tensors and ODFs and various other output files. BDP can read diffusion images in NIfTI-1 format. Please see supported file-formats for more details. It is recommended, but not required, to copy all of the required files to a separate directory for diffusion processing. The output files are written to the directory where the bias-field corrected MPRAGE image is located.

1. Check this list of requirement details to verify that your diffusion data is appropriate for BDP processing.
2. If you have not already done so, download and install MATLAB Compiler Runtime (MCR) release R2015b (9.0) for your operating system using links below.

   (The BDP scripts assume that the MCR is installed in a default location; if this is not the case, open the script (bdp.sh) in a text editor and change the BrainSuiteMCR variable to point to the correct installation.)

3. If you have not already done so, download and install C/C++ runtime libraries for your operating system:
   • Windows: Visual C++ runtime package from Microsoft website (64-bit only).
   • Mac: Install Xcode to get all runtime libraries.
   • Linux:(Usually pre-installed) Install libstdc++6 & its dependencies for your distribution.
4. Open Terminal (or Command Prompt)
   In Windows, the Command Prompt is found by clicking the Start Menu, All Programs, and then the Accessories folder. The Terminal application in Mac OS X is found in the Utilities directory in the Applications menu. How to open a terminal in Linux is distribution-specific, so search online for your distribution and how to open a terminal (often it is located in an “Accessories” or “System Tools” folder in the application menu).

   Windows Command Prompt showing a sample BDP command

5. Run BDP
   Depending on the format of your diffusion images and type of distortion correction required, the BDP script can be run in different ways as explained below. For details, please check exhaustive list of all the available flags and their descriptions on the BDP flags page.
   Please replace bdp.exe with full path of BDP executable in examples below. E.g. On Windows, replace bdp.exe with C:UsersnameBrainSuite16a1bdpbdp.exe.

   Using NIfTI input:
   BDP can read 4D NIfTI files as diffusion data input, which can be specified with the --nii flag. In this mode, the following files are required:

   1. fileprefix.bfc.nii.gz – bias-field corrected MRI image, saved by BrainSuite extraction sequence with .bfc.nii.gz extension.
   2. Diffusion images in 4D NIfTI format – saved as .nii or .nii.gz extension
   3. Gradient file – usually saved as plain text files with .bvec extension which contains diffusion gradient directions (example here). BDP assumes that the gradient directions are specified in voxel coordinates of the diffusion image. If not, the resulting tensors and ODFs produced may not be properly aligned to the anatomy of the subject.
   4. b-values file – usually saved as plain text files with .bval extension which contains b-values of diffusion scan.

   Windows:

   Linux and Macintosh:

   Where <BFC File> is the filename of the .bfc.nii.gz file, <4D DWI NIfTI> is the filename of the diffusion weighted image in NIfTI format, <Gradient File> is the filename of the gradient (bvec) file, and <B-Value File> is the filename of the b-value file or the value in s/mm² if you do not have this file.

   Example
   Assume all required files are in the directory C:Usersnamesubjectdiffusion_processing as such:

   To run BDP with default settings, run the script as (all on a single line):

   Or to estimate both ODF and tensor data, run:

   Optional flags

   A list of all the available flags and their detailed description are available on the BDP flags page.

This is a short post detailing how I installed Emacs and configured an environment for maintaining multiple configurations (on my MacBook Pro).I wanted to write the post because I have been on a roller coaster getting an Emacs install that provides all of the functionality that I want (maybe even need!).

Some Emacs installs (e.g. emacs from homebrew) are not recognised by the yabai tiling window manager and don't tile properly.This really started to bug me so I invested a hefty chunk of time (in classic Emacs style) to find a solution.I stumbled across Emacs-plus which solved the issue but left me with another…I use the pdf-tools package through the pdf-tools spacemacs layer for viewing all my pdfs; writing LaTeX docs (using org-mode and/or auctex), reading books, reading papers (using org-ref) etc.Unfortunately, both of these installs don't support retina pdf quality in PDFView (pdf-tools).So I set out on a second mission to get my myself a high res pdf viewing experience within Emacs.

Many GitHub issues later and The Emacs Mac Port came to the rescue.This is an excellent blog post detailing how The Emacs Mac Port (which I installed using Homebrew from this repo) greatly improves Emacs’ functionality with MacOS.In particular, it provides a lot of native GUI support.

I personally don't like having a title bar on my beautiful editor so I choose not to install it.I think I read somewhere that it might interfere with tiling window managers as well and we can't be having that, so let's install it without,

and to make sure that we are using the right install be sure to link emacs-mac with,

Now that we are using The Emacs Mac Port we need to add the following to our config file (user-config in spacemacs) if we want to enjoy the fruits of our labour,

I also like PDFView to open with the pdf fit to the screen (show 1 page) so I also added the following,

Chemacs

Chemacs is an Emacs profile switcher that makes it easy to run multiple Emacs configs side by side.I am currently running six Emacs configurations,

1. New Spacemacs Base (Develop Branch)
   • This is a new config that I am setting up using just spacemacs-base instead of full spacemacs. I want to understand all of the packages I am using and install only the ones I need, thus avoiding a lot of bloat.
2. New Spacemacs Base (Master Branch)
   • This is the same config file but running on spacemacs master instead of the develop branch.
3. Literate Org Config File
   • This is the same configuration but written in an Org file with lots of documentation. I use tangle/detangle to produce emacs lisp files from the org file. I haven't decided if I want to fully invest in a literate config file so this is a nice way to experiment.
4. Vanilla Emacs
   • Although I love spacemacs I am eager to build a full Emacs config from scratch and this config is my attempt.
5. Spacemacs Old Develop
   • This is my old (full) spacemacs config running on the develop branch.
6. Spacemacs Old Master
   • This is my old spacemacs config running on master.

It's super easy to setup, just clone the repo and run the install script.I don't think I need to repeat the instructions that are listed in their README.Once you have it setup the main functionality comes from two files.First there is the ~/.emacs-profiles.el file where you define all of your different configurations.This is what my ~/.emacs-profiles.el file looks like,

1. Chemacs will load the init.el file from the user-emacs-directory,
   • you can change the file name/path by setting the cutom-file variable.
2. You can set each configuration file to use a different server name with the server-name variable,
   • this is super useful if you want to exploit emacsclient for a speedy startup, something I am currently working on!
3. A set of environment variables with env,
   • I use this to set the SPACEMACSDIR variable which tells spacemacs where to look for extra customisation's.

The other Chemacs file is the ~/.emacs-profile file where you set the default config to use.Mine is currently,

Bfc Playground Mac Os Catalina

Another great benefit of Chemacs is that it also makes it super easy to version control all of your emacs configuration files, layers, snippets etc.I keep all of mine in my version controlled ~/.dotfiles folder with their own dedicated folders.For example I have put all of my snippets (for use with yasnippet) inside a private folder~/.dotfiles/spacemacs-base-new/private/snippets and all of my layers are inside ~/.dotfiles/spacemacs-base-new/layers.To make my configs more portable I also set the layer path variable in the dotspacemacs/layers function using,

and set any references to the private directory with something like,

Emacs Server/Client

The Emacs server is super useful if your config file takes a couple of seconds to load.I know that some of mine do and I hate waiting…

Luckily we can run an Emacs server with the first instance we open and then connect to this server using emacsclient when “opening” subsequent instances.These new instances open almost instantaneously for me.

To get this working you first have to start the server.I have been struggling to get it setup with the spacemacs server config so I turn off all of the spacemacs server functionality,

and start my own by adding,

to my user-config.

Bfc Playground Mac Os Download

We now need to know if an Emacs server is running so that we can either connect to it or start a new Emacs instance if not.To get this working I use the following shell script.

You might have to change the EMACS and EMACS_CLIENT variables depending where brew linked your install.Let's give our shell script permissions,

Bfc Playground Mac Os X

and set an alias e “emacs” by executing the following (assuming you use zsh),

If you use bash then it will be,

Bfc Playground Mac Os 11

but you should consider switching!We can now open new Emacs instances by typing e <file-name> or simply e into terminal.

I take this one step further as I use skhd (a simple hotkey daemon for macOS) to open my default Emacs config (utilising emacsclient) with a simple keybinding.Creating an extra script was probably overkill but it works so I am happy.The only difference here is that no filename is passed to emacsclient so we instead ask it to open a new frame.

Again let's give it permissions,

I then set CMD m to run the shell script by placing the following in my ~/.config/skhd/skhdrc file,

This will either connect to the server of a previously running instance and open a new frame or open a new Emacs instance and start a server.

Fantastic, we now have a super speedy Emacs setup that we can easily use with six different configurations.If anyone has any great ideas for improving anything I have shown here I am all ears 👂.Happy hacking..

BFC Playground Mac OS