Note
So for today’s article, let’s go over how to change the default download folder on the Mac! Luckily, the process of changing the default download directory pretty similar in the three main Mac browsers. Change the Default Download Location in Safari. Open the Safari app and click on the Safari drop-down menu at the top left. Replace /Downloads with your actual path and Anaconda3-2020.02-MacOSX-x8664.sh with actual name of the file you downloaded. The installer prompts “In order to continue the installation process, please review the license agreement.”.
Once you have downloaded the installer, open a Terminal (look in the Utilities folder in Applications), change to the folder containing the downloaded file (for example if you downloaded to your Desktop): cd /Desktop (On Mac OS X 10.5, Safari defaults to downloading files into /Downloads) and run it with: sh fslinstaller.sh. Mac OS X doesn’t have an obvious way to view the exact text based path to a folder (otherwise known as a directory) in the finder window. You can have it show a graphical path, but getting just the text based path to a directory (for use in the Terminal for example) requires a couple of extra steps. Get File Path allows you to copy to the clipboard the path of a file or folder dropped on it, after automatic application of various programmable transformations. It works with any kind of file.
Using Anaconda in a commercial setting? You may need to use Anaconda Commercial Edition. If you have already purchased Commercial Edition, please proceed to the Authenticating Commercial Edition section after completing your installation here.
Haven’t purchased Commercial Edition yet? Visit https://anaconda.cloud/register to get started.
You can install Anaconda using either the graphical installer (“wizard”) or thecommand line (“manual”) instructions below. If you are unsure, choose the graphical install.
macOS graphical install¶
- Download the graphical macOS installer for your version of Python.
- RECOMMENDED: Verify data integrity with SHA-256.For more information on hashes, see What about cryptographic hash verification?
- Double-click the downloaded file and click continue to start the installation.
- Answer the prompts on the Introduction, Read Me, and License screens.
- Click the Install button to install Anaconda in your ~/opt directory (recommended):
- OR, click the Change Install Location button to install in another location (not recommended).On the Destination Select screen, select Install for me only.NoteIf you get the error message “You cannot install Anaconda in this location,” reselect Install for me only.
- Click the continue button.
- Optional: To install PyCharm for Anaconda, click on the link to https://www.anaconda.com/pycharm.Or to install Anaconda without PyCharm, click the Continue button.
- A successful installation displays the following screen:
- Verify your installation.
Using the command-line install¶
Use this method if you prefer to use a terminal window.
- In your browser, download the command-line version of themacOS installer for your system.
- RECOMMENDED: Verify data integrity with SHA-256.For more information on hash verification, see cryptographic hash validation.
- Open a terminal and run the following:
NoteReplace/path/filename
with your installation’s path and filename. - Install for Python 3.7 or 2.7:
- For Python 3.7 enter the following:
- For Python 2.7, open the Terminal.app or iTerm2 terminal application and then enter the following:
NoteInclude thebash
command regardless of whether or not you are using the Bash shell.NoteReplace~/Downloads
with your actual path andAnaconda3-2020.02-MacOSX-x86_64.sh
with actual name of the file you downloaded. - The installer prompts “In order to continue the installation process, please review the license agreement.”Click Enter to view the license terms.
- Scroll to the bottom of the license terms and enter yes to agree to them.
- The installer prompts you to Press Enter to confirm the location, Press CTRL-C to cancel the installationor specify an alternate installation directory. If you confirm the default location,it will display
PREFIX=/home/<user>/anaconda<2or3>
and continue the installation.NoteUnlike the graphical install, installing the shell file will place it in ~/anaconda<2 or 3> by default,not ~/opt. This is due to limitations with installing .pkg files on macOS Catalina.Installation may take a few minutes to complete.NoteWe recommend you accept the default install location. Do not choose the path as /usr for theAnaconda/Miniconda installation. - The installer prompts “Do you wish the installer to initialize Anaconda3by running conda init?” We recommend “yes”.NoteIf you enter “no”, then conda will not modify your shell scripts at all.In order to initialize after the installation process is done, first run
source<pathtoconda>/bin/activate
and then runcondainit
.NoteIf you are on macOS Catalina, the new default shell is zsh.You will instead need to runsource<pathtoconda>/bin/activate
followed bycondainitzsh
. - The installer displays “Thank you for installing Anaconda!”
- Optional: The installer describes the partnership between Anaconda and JetBrains andprovides a link to install PyCharm for Anaconda athttps://www.anaconda.com/pycharm.
- Close and open your terminal window for the Anaconda installation to take effect.
- To control whether or not each shell session has the base environmentactivated or not, run
condaconfig--setauto_activate_baseFalseorTrue
. To run conda from anywhere without having the base environmentactivated by default, usecondaconfig--setauto_activate_baseFalse
.This only works if you have runcondainit
first.Notecondainit
is available in conda versions 4.6.12 and later. - Verify your installation.
What’s next?¶
Get started programming quickly with Anaconda in the Getting started with Anaconda guide.
Thanks to Robert Coghill for sponsoring the Apple port.
Contents:
![Edit Edit](/uploads/1/1/8/9/118958580/676680143.png)
- FSL install script
Prerequisites
Before you install FSL you should first ensure that you have the X11 windowing system installed. To do this, look for the X11 application in the Utilities folder within the Applications folder (switch to the Finder and hit Apple-Shift-U to open the Utilities folder); by default versions of Mac OS X prior to 10.5 doesn't normally come with this installed (you'll almost certainly need X11 later for things other than FSL anyway).
If you do not have X11 then install it from the OS X Install CD. Insert the CD, open it in the Finder, scroll down to the Optional Installs.mpkg package and double click to launch the installer (in Mac OS X 10.5, the package is in the Optional Installs folder). Click through until the custom install window appears, expose the Applications section and select X11. Now click on 'Install'
![Download Directory Path For Mac Download Directory Path For Mac](/uploads/1/1/8/9/118958580/452071900.png)
FSL Install Script
An automated installer, fsl_installer.sh is available to carry out the installation (or application of a patch). In addition it will install FSLView into /Applications, automatically configure your environment to enable you to run FSL and (on Mac OS X 10.4) will configure the Apple Terminal application to allow the launching of X11 applications from it. Finally, if you use Matlab it will configure your startup.m file to allow you to use the FSL Matlab functions.
- fsl_installer.sh - Version 1.6 09/02/2012
Running the installer
Once you have downloaded the installer, open a Terminal (look in the Utilities folder in Applications), change to the folder containing the downloaded file (for example if you downloaded to your Desktop):
(On Mac OS X 10.5, Safari defaults to downloading files into ~/Downloads)
and run it with:
Assuming that this folder also contains the FSL distribution tar file and you wish to install into /usr/local then just press Return when the installer asks a question, to accept the defaults. Be aware that you may need Administrator priviledges to install into certain folders on your computer - /usr/local being an example, the installer will ask for your password if necessary to allow this.
For more information on controlling the installer, run it with the -h option.
Configuring your account for FSL usage using the install script
In addition to installing the FSL programs, the install script is also capable of configuring your user account to enable you to run the FSL programs. If your user account was used to run the installer when installing the FSL programs, this will have already been done, but you may also want to configure additional accounts. To do this, log in as the user wishing to run FSL and execute the installer with the -e option, eg:
Checking the installation
Test that the environment and command line tools are set up correctly by doing the following:
- Quit the Terminal program and start it again
- Check that your environment is correct by typing: This should display the name of the directory that you installed FSL in.
- Check that your path is correct by typing: which should display a line like: (although the version number might be different).
In general, to run the FSL tools from the command line (within a terminal) you need to enter the program name in lower case (e.g. bet). Typing a command on its own (without any arguments or options) gives you a help message for that command.
A more complete test of the FSL installation can be run at this pointby using the testing and evaluation suite FEEDS.
Running the GUIs
Mac OS X 10.4
Once you have checked the environment and command line programs, as described above, then start X11 (click on it in the Utilities folder inside the Applications folder). All of the FSL GUIs should now work. To run a GUI version of a program you can either type its capitalised name with an additional '_gui' appended in the terminal (e.g. Bet_gui), or you can start the main FSL GUI by just typing fsl.
Mac OS X 10.5
There is no need to launch X11.app before starting any of the FSL GUIs, the X11 system automatically launches. To run a GUI version of a program you can either type its capitalised name with an additional '_gui' appended in the terminal (e.g. Bet_gui), or you can start the main FSL GUI by just typing fsl.
If you have upgraded from 10.4, then you may have a .bash_profile (or .tcshrc or .cshrc) that breaks this behaviour. If you installed using the fsl_installer.sh script then download the current version, fsl_installer.sh, and re-run using the -e option from a terminal:
assuming that your web browser downloads to the folder ~/Downloads.If you have manually added this to your shell setup file then look for a line that changes/sets the DISPLAY environment variable and remove it. New shells will then behave as expected.
Also note that at this time, Apple's X11.app as shipped, has a large number of bugs and performance issues. Until such time as an offical release corrects these problems, you may see significant improvements by installing the testing release available at http://www.x.org/wiki/XDarwin (follow the instructions for a Binary installation).
Using Matlab libraries
FSL ships with several Matlab scripts for loading Analyze files. These libraries are dependant on FSL environment variables which aren't set in the Mac OS X Desktop environment, so won't run in a Matlab session started from the /Applications/MATLAB.app launcher. There are two options:
- Run Matlab from a correctly configured Terminal (assuming Matlab 7.4 - adjust as appropriate for your version) or
- Configure the FSL environment variable in your ~/matlab/startup.m file (create it if it doesn't already exist) - add the following (assuming FSL installed in /usr/local):
Further help
If any problems occur when installing or running the FSL tools, please consult the FSL FAQ. This also contains instructions on how to join and use the FSL email list to ask specific questions which are not covered in the FAQ.
Edit Path Mac
Manual Installation
Mac Os Path
- Verify the download
- Visit our checksums page to download the MD5 sum file that matches the
.tar.gz package you have downloaded. Make sure that the.md5 file is in the same directory as the downloaded FSL distribution file. - Open up a Terminal (you can find this application in Utilities folder inside the Applications folder).
- In the terminal, change to the directory where you downloaded the FSL distribution, e.g.
- Check the file with NB ` is on the key to the left of Z on the UK Mac keyboard, or to the left of 1 on the US Mac keyboard
- If there is a problem with the download then you will receive a message like:
- Visit our checksums page to download the MD5 sum file that matches the
- Unpack the FSL distribution
- Open up a Terminal (you can find this application in Utilities folder inside the Applications folder).
- In the terminal, change to the directory where you want FSL installed, e.g.
- Unpack the fsl download file - for example, if you downloaded it onto your Downloads folder, (omit the z in the -zxvf if your computer has already uncompressed the tarfile for you). This will create a directory called fsl in the current directory which will contain all the required files for FSL and FSLView. Note that you might need to add sudo to the start of the tar command if you don't automatically have the right to create files in /usr/local.
- Install the applications
- To get a clickable application icon FSLView, open a file browser in the top-level fsl directory, e.g. and drag the fslview.app directory into your Applications folder or your Desktop.
- Find out which shell you are running. In a terminal, type: the output will be either a list of commands, in which case you are using the bash shell, or an error saying 'command not found' or similar message, in which case you are using the tcsh or csh shell.
- Set up your user environment.
If you are using the bash shell (the default)
- In a running terminal type: This will bring up a TextEdit window
- Select Make Plain Text from the Format menu if it is available (if only Make Rich Text is there then do nothing as it is already in plain text mode)
- In the window type the following lines at the end of the document (or better still, use copy and paste to do this): Note that the second line starts with a dot (i.e. full stop or period), then a space, then ${FSLDIR}/etc/fslconf/fsl.sh - the dot and space are very important!For Mac OS X 10.4 and earlier (NOT Mac OS X 10.5), also include the following:
- Change the line FSLDIR=/usr/local/fsl and replace /usr/local/fsl with the directory name of the place where you installed FSL.
- Save the file and exit TextEdit
If you are using the tcsh or the csh shell
- In a running terminal type: This will bring up a TextEdit window
- Select Make Plain Text from the Format menu if it is available (if only Make Rich Text is there then do nothing as it is already in plain text mode)
- In the window copy and paste the following in at the end of the document: For Mac OS X 10.4 and earlier (NOT Mac OS X 10.5), also include the following:
- Change the line setenv FSLDIR /usr/local/fsl and replace /usr/local/fsl with the directory name of the place where you installed FSL.