Install OSX processing tools

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Mac OS X Tools - Info


This document was written to help you find and install most of the tools we use here at the Brainmapping Center (on Mac OS X 10.2 ONLY). Please read carefully, follow the instructions and you will be up and running in no time (well, there is the download time...)

  1. What tools are we talking about?
  2. Where do I find the tools?
  3. OK, but which tools do I need and how do I install them?

What tools are we taking about?

Here at the Brainmapping Center we use the following tools (listed in no specific order):

  • FSL - "a comprehensive library of functional and structural brain image analysis tools."
  • AFNI - "a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data."
  • UCLA Tools - a set of various tools (command line only) created by Mark Cohen here at the Brainmapping Center.
  • AIR - a set of tools that are used for "automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities."
  • xds - a very popular and widely used display tool for MGH-style format image data.
  • MATLAB and SPM - no, we are not going to distribute MATLAB or SPM here, but we are going to tell you how to make it work on OS 10.2.
  • X11 - a free (at least for now) implementation of the X Window System for Mac OS X created by Apple and based on Xfree86. This is needed to run FSL, AFNI, MATLAB and xds.

We also provide samples of resource files:

  • Resource Files - Folder'RC_Files' at www.brainmapping.org contains examples of resource files some of which you will need and some that are just nice to have (they can make life a little bit easier). NOTE: these files should be saved in your home directory, and they should have a . (dot) in front of the name, but we could not load them like that here (they would not show on out ftp site). Instead these files are loaded as simple text files, and when you click on them they will display in the browser. You can view them and then modify your existing resource files, or you can download them (or you can just cut-and-paste from your browser directly to a text editor of your choice - make sure that you save as plain text). If you download them, first rename them from 'something' to '.something', and then save them in your home directory.
    1. tcshrc (.tcshrc) or cshrc (.cshrc) - these are important and you should have one in your home directory (you don't need both; in fact, if you do, only one will be read and executed (I believe .tcshrc takes precedence) that sets a correct path to all of the tools and also uses an alias file for the shortcuts. You can easily set up you .tcshrc (or .cshrc) file with the same paths because the tools you have installed are in the same directories as in this example file. You can also find an example of .cshrc (could easily be called .tcshrc) file here, which does not set paths. By setting paths as in the first example, you will be able to start any of your tools from the command line. If you try to start afni (for example) and type 'afni', but the system tells you 'command not found' your problem is probably in incorrect path. If you do not set your path this way, you can still start your tools, but you need to specify the whole path to the executable( e.g. type /usr/local/bin/afni/afni to launch afni).
    2. xinitrc (.xinitrc) NOT USED WITH X11- this is an initialization file for X Windows and this one in particular is used if you are using mwm as your window manager. The commands in this file will be executed when your XWindows are starting (this one will start mwm and open three windows). There are many more commands that you can put here, but this is the minimum.
    3. afnirc (.afnirc) - some environment variables. Not needed, but will not hurt.
    4. gnuplot (.gnuplot) - some variables for gnuplot. Again, not necessary, but nice to have.
    5. alias (.alias) - some example shortcuts. Note that this file is called from .tcshrc or .cshrc. This is useful if you are using some commands repeatedly - saves time on typing. You don't need this file, but it helps.

Where do I find the tools?

You can find links to all the tools on the Installation Instructions page.

OK, but which tools do I need and how do I install them?

For this too, see Installation Instructions.

Installation Instructions

What to do if you want to:

  1. Install Tools on 10.3 (Panther) NEW - (X)MedCon for Panther! (updated 05/10/04)
  2. Install Tools on 10.2 (Jaguar) - somewhat supported
  3. Upgrade to Jaguar (10.2) from 10.1 - no longer supported
  4. Install Tools on 10.1 - no longer supported

IMPORTANT NOTE: If not otherwise specified, all of the downloads will be in either *.zip, *.sit or *sea format. 'zip' and 'sit' files can be unzipped by doubleclicking (if they don't unzip automatically after downloading); but if you try doubleclicking on a 'sea' file it will try to open an application in classic mode. You don't want that. To go around this problem - drag a 'sea' file onto the stuffit expander - that will do the trick. I have not been able to figure out why this is happening (not that I spent nights working on the issue), so if someone figures it out - let me know!

Install Tools on 10.3 (Panther)

  1. X-Windows need to be installed first! If you plan on using only UCLA Tools and/or AIR, you don't need X-Windows!
    1. Apple now ships X11 with Panther. However, you have to do a custom installation, and check X11 to be installed. If you have not done so, you can download X11 directly from Apple. X11 will be installed in the /Applications/Utilities folder.
  2. FSL
    1. Download - go to the FSL Download Page, fill out the form, select a Mac OS X version and download. At this point go grab a cup of coffee because this will take some time.
    2. With the latest version of FSL, the format of the distributed file has change. It once was a *.tar.gz file, but now, it is a disk image that will mount fsl folder on your Desktop, as a separate drive. To install do
      1. Open the mounted drive and copy the 'fsl' folder on your desktop.
      2. Open a Terminal window move that folder to /usr/local/bin:

        sudo mv ~/Desktop/fsl /usr/local/bin/fsl

      3. There are two more items in the mounted drive. Those are the shortcuts to FSL and FSLview, and if you copy them over to your Desktop, doubleclicking on them will automatically bring up the FSL menu window, or FSLview window, repectively. This will also automaticaly launch X11.
    3. Set up the path - add the path (/usr/local/bin/fsl/bin) in your .tcshrc file. If you don't have a .tcshrc, there is an example of one in the 'RC FILES' folder. You can just copy all of the lines into your new .tcshrc file. Type 'source .tcshrc' from the xterm so that the changes can take effect and then start fsl by typing 'fsl' on the command line.
  3. AFNI
    1. From the 'Utilities' folder download libs.pkg.sit and openmotif-2.2.0-OSX.pkg.sit files, and install. These are required for afni to run under OS X and X-Windows.
    2. There are two ways to install AFNI - using 'wget'(this one offers easier updates) or downloading tar files (this one is faster, see item 3).
      1. 'wget' is recommended for easy installation (and later updates) of AFNI. First, download 'wget' from the Utilities folder (wget.tar.gz), move it to /usr/local/bin and unzip it:

        sudo mv wget.tar.gz /usr/local/bin/
        cd /usr/local/bin
        sudo gunzip wget.tar.gz
        sudo tar xvf wget.tar


For those of you who think this is too easy: you can also get 'wget' from Fink website. You will first have to install Fink software and then download 'wget' using that software. To install Fink on your Panther, visit the 10.2 Fink installation page. Once this is done you can use Fink to download 'wget' binaries (or any any other package supported by Fink).

      1. Assuming that your 'wget' works, you can now use it to install afni binaries directly from AFNI website. The command is the following:

        sudo wget -nv -m -np -nH -P $AFNIDIR --cut-dirs=4 http://afni.nimh.nih.gov/pub/dist/bin/macosx_10.3/

        where AFNIDIR is /usr/local/bin/afni. If you set up your .tcshrc file in step 2 (while installing fsl) your AFNIDIR is already set (try typing 'echo $AFNIDIR' on the command line to check whether it exists; it should return '/usr/local/bin/afni'). If you didn't do so, now is the time. Follow step 3 of FSL installation above - the easiest thing is just to copy the whole example tcshrc file into your own .tcshrc file.

**NOTE**: AFNI suite changes very frequently. If you type 'afni_vcheck' you can see what version of the suite you have and what is the latest one available. To update afni, simply use the same 'wget' command as above. This should take much less time than the initial download.

      1. 'wget' can be quite slow, specially if you are installing AFNI for the first time. So, if you don't want to wait, download the tar file from AFNI.html, move it to /usr/local/bin and unzip. NOTE: your browser might want to automatically unzip the tar file, but that will not work because of the way this file was created. You might have a folder created on your desktop (or wherever you have downloaded the tar file) but it will be empty and you can delete it.

        sudo mv AFNIarchive.tar.gz /usr/local/bin/
        cd /usr/local/bin
        sudo gunzip AFNIarchive.tar.gz
        sudo tar xvPf AFNIarchive.tar
        NOTE: IT IS VERY IMPORTANT THAT YOU USE 'P' (tar xvPf...) OTHERWISE IT WILL NOT INSTALL IN THE RIGHT PLACE!

This archive file will be updated one a week, so you might not get the latest version.

      1. If you plan to use the Talairach atlas that comes with AFNI, you need to download those files separately. Download files TTatlas+tlrc.BRIK.gz and TTatlas+tlrc.HEAD, unzip the first one, and move them to /usr/local/bin/afni/. (You can also find those files at the afni home page)
  1. AIR
    1. Download AIR*-type2.pkg.sit file (from folder 'Tools' on www.brainmapping.org/Downloads ) and install. This will install all of AIR tools in /usr/local/bin/AIR*
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  2. xds
    1. Download xds.pkg.sit file (from folder 'Tools' on www.brainmapping.org/Downloads ) and install. This will install xds tools in /usr/local/bin/xds
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  3. UCLATools
    1. UCLATools*.tar.gz - you can find this file in the binary downloads directory. Use this if you are installing the tools for the first time. To install the tools, download the file, move to the directory where the file was downloaded and:

      sudo mv UCLATools*.tar.gz /usr/local/bin/
      cd /usr/local/bin
      sudo gunzip UCLATools*.tar.gz
      sudo tar xvf UCLATools*.tar

      You don't need to download this one every time there is an update. Just find the corresponding binary in the list and download it.
    2. individual tools (binaries) - this is useful for updates. To download a file you will need to right-click and then select 'download link to disk' (if you just left-click it will try to open a file in the browser and that's no good). Save the file in a convenient place, and then move to /usr/local/bin/UCLATools/ (you will have to do this using the terminal - unfortunately the protected files are not visible in finder; actually they are but there is a permissions problem so you will still need to move the file using the terminal - sudo mv /usr/local/bin/UCLATools/).
  4. MATLAB and SPM
    1. MathWorks released MATLAB version 13 that can run under OS X. They have released it initially for 10.1 and then when Jaguar came out, MATLAB did not work. MathWorks fixed this recently, and now there is a patch that you need to download and install that will enable your MATLAB 13 under OS 10.2. You can read all about that at http://www.mathworks.com/support/solutions/data/33053.shtml. Once you have MATLAB up and running, SPM should be easy to install. Unfortunately as I don't use SPM, I have not tried this (yet?) so I cannot offer any help. However, SPM website might offer some insight on how to accomplish this.
  5. (X)MedCon(X)MedCon
    1. Download the xmedcon-0.9.1.pkg.sit, doubleclick to unpack and then doubleclick again to install. You will need administrative privileges to install. (X)MedCon will be installed in /usr/local/bin/xmedcon.
    2. Add the following path to your .tcshrc file: /usr/local/bin/xmedcon/bin.

Install Tools on 10.2 (Jaguar)

At first these instruction might seem a bit overwhelming, but if you follow them step by step, you should not have any (major) problems.

  1. X-Windows need to be installed first! If you plan on using only UCLA Tools and/or AIR, you don't need X-Windows!
    1. 01/12/04. UPDATE: At the link below, you can only get X11 for 10.3, which will NOT work on 10.2. Older versions of X11 can be found at www.versiontracker.com, and X11 for 10.2 can be found here (make sure you are downloading version 0.3).
    2. 04/01/03. We are now using Apple's X11 for OS X which is available from Apple's website. It is currently in Beta version 3 and it is based on XFree86. All you have to do is download and install, and you are ready to go. (Do not use a .xinitrc file with X11).
  2. FSL
    1. 01/12/04. UPDATE: The format of the distributed FSL package has changed and the instructions below are no longer valid. See above for new installation instructions.
    2. Download - go to the FSL Download Page, fill out the form, select a Mac OS X version and download. At this point go grab a cup of coffee because this will take some time.
    3. Unpack - Don't use the automatically unzipped folder - if one was created (I have seen some strange behavior with that when all the symbolic links were empty). Instead, move the file to /usr/local/bin and unzip it (use the following commands):

      sudo mv ???whatever???.tar.gz /usr/local/bin/
      cd /usr/local/bin
      sudo gunzip ???whatever???.tar.gz
      sudo tar xvf ???whatever???.tar


    4. Set up the path - add the path (/usr/local/bin/fsl/bin) in your .tcshrc file. If you don't have a .tcshrc, there is an example of one in the 'RC FILES' folder. You can just copy all of the lines into your new .tcshrc file. Type 'source .tcshrc' from the xterm so that the changes can take effect and then start fsl by typing 'fsl' on the command line.
  3. AFNI
    1. From the 'Utilities' folder download libs.pkg.sit and openmotif-2.2.0-OSX.pkg.sit files, and install. These are required for afni to run under OS X and X-Windows.
    2. There are two ways to install AFNI - using 'wget'(this one offers easier updates) or downloading tar files (this one is faster, see item 3).
      1. 'wget' is recommended for easy installation (and later updates) of AFNI. First, download 'wget' from the Utilities folder (wget.tar.gz), move it to /usr/local/bin and unzip it:

        sudo mv wget.tar.gz /usr/local/bin/
        cd /usr/local/bin
        sudo gunzip wget.tar.gz
        sudo tar xvf wget.tar


For those of you who think this is too easy: you can also get 'wget' from Fink website. You will first have to install Fink software and then download 'wget' using that software. To install Fink on your Jaguar, visit the 10.2 Fink installation page. Once this is done you can use Fink to download 'wget' binaries (or any any other package supported by Fink).

      1. Assuming that your 'wget' works, you can now use it to install afni binaries directly from AFNI website. The command is the following:

        sudo wget -nv -m -np -nH -P $AFNIDIR --cut-dirs=4 http://afni.nimh.nih.gov/pub/dist/bin/macosx_10.2/

        where AFNIDIR is /usr/local/bin/afni. If you set up your .tcshrc file in step 2 (while installing fsl) your AFNIDIR is already set (try typing 'echo $AFNIDIR' on the command line to check whether it exists; it should return '/usr/local/bin/afni'). If you didn't do so, now is the time. Follow step 3 of FSL installation above - the easiest thing is just to copy the whole example tcshrc file into your own .tcshrc file.

**NOTE**: AFNI suite changes very frequently. If you type 'afni_vcheck' you can see what version of the suite you have and what is the latest one available. To update afni, simply use the same 'wget' command as above. This should take much less time than the initial download.

      1. 'wget' can be quite slow, specially if you are installing AFNI for the first time. So, if you don't want to wait, download the tar file from AFNI.html, move it to /usr/local/bin and unzip. NOTE: your browser might want to automatically unzip the tar file, but that will not work because of the way this file was created. You might have a folder created on your desktop (or wherever you have downloaded the tar file) but it will be empty and you can delete it.

        sudo mv AFNIarchive.tar.gz /usr/local/bin/
        cd /usr/local/bin
        sudo gunzip AFNIarchive.tar.gz
        sudo tar xvPf AFNIarchive.tar
        NOTE: IT IS VERY IMPORTANT THAT YOU USE 'P' (tar xvPf...) OTHERWISE IT WILL NOT INSTALL IN THE RIGHT PLACE!

This archive file will be updated one a week, so you might not get the latest version.

      1. If you plan to use the Talairach atlas that comes with AFNI, you need to download those files separately. Download files TTatlas+tlrc.BRIK.gz and TTatlas+tlrc.HEAD, unzip the first one, and move them to /usr/local/bin/afni/. (You can also find those files at the afni home page)
  1. AIR
    1. Download AIR*-type2.pkg.sit file (from folder 'Tools' on ftp.brainmapping.org ) and install. This will install all of AIR tools in /usr/local/bin/AIR*
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  2. xds
    1. Download xds.pkg.sit file (from folder 'Tools' on ftp.brainmapping.org ) and install. This will install xds tools in /usr/local/bin/xds
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  3. UCLATools
    1. UCLATools*.pkg.sit - (Tools/UCLATools folder) all of the command line tools as a package. Use this if you are installing the tools for the first time. All of the tools will be installed in /usr/local/bin/UCLATools. You don't need to download this one every time there is an update. Just find the corresponding binary in the list and download it.
    2. individual tools (binaries) - this is useful for updates (see the top of the ftp page, or the UpdateHistory.html file for notes about recent updates). If you are using Safari as your browser, this link will open a new finder window where you will be able to see all files. To copy them to your computer, just drag them over to your Desktop. If you are using IE (still using IE? shame on you!) the list of files will appear as a list in your browser window. To download a file you will need to right-click and then select 'download link to disk' (if you just left-click it will try to open a file in the browser and that is no good). Save the file in a convenient place, and then move to /usr/local/bin/UCLATools/ (you will have to do this using the terminal - unfortunately the protected files are not visible in finder).
  4. MATLAB and SPM
    1. MathWorks released MATLAB version 13 that can run under OS X. They have released it initially for 10.1 and then when Jaguar came out, MATLAB did not work. MathWorks fixed this recently, and now there is a patch that you need to download and install that will enable your MATLAB 13 under OS 10.2. You can read all about that at http://www.mathworks.com/support/solutions/data/33053.shtml. Once you have MATLAB up and running, SPM should be easy to install. Unfortunately as I don't use SPM, I have not tried this (yet?) so I cannot offer any help. However, SPM website might offer some insight on how to accomplish this.

Upgrade to Jaguar (10.2) from 10.1

NOTE: we no longer support this.

This is actually the easiest one. Here, we will assume that you have upgraded to 10.2.x (whatever the most current upgrade to 10.2 is) and that you had Xfree86 4.2 (and other tools) up and running on 10.1.x (if you don't have that, you need to follow instructions on how to install the tools on 10.2 from scratch). If so, all you need to is:

  1. Download a patch for Xfree86 from the 'Utilities' folder (here at www.brainmapping.org/Downloads) - the file that you need is Xfree86_4.2.0.1-10.2.zip, doubleclick and follow the instructions.
  2. Modify your .tcshrc file: if you had the following line in your .tcshrc file -
    setenv MANPATH "${MANPATH}:/usr/X11R6/man" change it to -
    if ( $?MANPATH ) then
    setenv MANPATH "${MANPATH}:/usr/X11R6/man"
    else
    setenv MANPATH /usr/X11R6/man
    endif
    (for an example look at the tcshrc file in the 'RC FILES' directory)
  3. Now, try starting your x-windows. It should behave as before. If X-Windows crashes on start, you can either open up your console window (you can find it in /Applications/Utilities) and try to troubleshoot the problem, or you could just reinstall Xfree86 - download and install XInstall_10.1.sit and then reinstall the patch. It should work now.
  4. If you have already installed MATLAB (or are planning to install MATLAB) you will have to apply a patch to the current MATLAB package for OS X. You can find all the details as well as downloads at: http://www.mathworks.com/support/solutions/data/33053.shtml

Install Tools on 10.1 from scratch

NOTE: we no longer support this.

I don't know why you want to do this since - but here it is. Word of caution though - you might run into problems because we (as well as creators of other tools used here) will not be supporting 10.1 any more.

  1. First you need to install X-Windows. If you plan on using only UCLA Tools and/or AIR, you don't need X-Windows!
    1. From the 'X Windows' folder at ftp.brainmapping.org, download XInstall_10.1.sit file and install (that's the basic installation of Xfree86 4.2 for Mac OS 10.1).
    2. From the same directory, download Xfree86_4.2.0.1-10.1.zip file and install (this is the upgrade to Xfree86 4.2.0.1 - fixes some bugs)).
    3. Your X Windows are operational at this point, but if you try to start it, you will see that it will open three very ugly windows - it is using the default window manager which is pretty primitive (twm). One step up is mwm (motif window manager), a little less 'simple' window manager that you might want to use. It can be found in the 'Utilities' folder. Download and install. It will be installed in /usr/X11R6/bin. Before you can use it you have to make it executable!! (sudo chmod a+x /usr/X11R6/mwm)
    4. Now, in order for X windows to know that you want it to use mwm, you will have to set up an initialization file. This file needs to live in your directory and it has to be called '.xinitrc' (note a 'dot' in the beginning of the name). You can put all sorts of things in there, but a simple initialization file is the best and you can find an example of one such 'simple' file in the 'RC FILES' folder (xinitrc). You can copy those line in your own .xinitrc file and your X Windows are ready to roll.
  2. FSL
    1. Download - go to the FSL Download Page, fill out the form, select a Mac OS X version and download. At this point go grab a cup of coffee because this will take some time.
    2. Unpack - Don't use the automatically unzipped folder - if one was created (I have seen some strange behavior with that when all the symbolic links were empty). Instead unzip the file by typing (in the directory where the file was downloaded):

      gunzip ???whatever???.tar.gz
      tar xvf ???whatever???.tar


      This will create a folder called 'fsl' that you now need to move over to /usr/local/bin. You can do this by typing (from the directory where you downloaded fsl to):

      sudo mv fsl /usr/local/bin/fsl
    3. Set up the path - add the path (/usr/local/bin/fsl/bin) in your .tcshrc file. If you don't have a .tcshrc, there is an example of one in the 'RC FILES' folder. You can just copy all of the lines into your new .tcshrc file. Type 'source .tcshrc' from the xterm so that the changes can take effect and then start fsl by typing 'fsl' on the command line.
  3. AFNI
    1. From the 'Utilities' folder download libs.pkg.sit and openmotif-2.2.0-OSX.pkg.sit files, and install. These are required for afni to run under OS X and Xfree86 4.2.
    2. Set up 'wget' for easy installation (and later updates) of AFNI (I strongly recommend you use wget, but the alternative exists and is explained in item 5). You can get wget from Fink website. You will first have to install Fink software and then download wget using that software. To install Fink on your OS 10.1, visit the Fink installation page. (This is the latest version of Fink, but also the last one for 10.1. Future versions will be for Jaguar only). Once this is done you can use Fink to download wget binaries (or any other package supported by Fink). If, for some reason, you decide you don't like Fink, you can try to get wget from http://sunsite.auc.dk/wget/.
    3. Assuming that your wget works, you can now use it to install afni binaries directly from AFNI website. The command is the following:

      sudo wget -nv -m -np -nH -P $AFNIDIR --cut-dirs=4 http://afni.nimh.nih.gov/pub/dist/bin/macosx_10.2/

      where AFNIDIR is /usr/local/bin/afni. If you set up your .tcshrc file in step 2 (while installing fsl) your AFNIDIR is already set (try typing 'echo $AFNIDIR' on the command line to check whether it exists; it should return '/usr/local/bin/afni'). If you didn't do so, now is the time. Follow step 3 of FSL installation above - the easiest thing is just to copy the whole example tcshrc file into your own .tcshrc file.
      NOTE: AFNI suite changes very frequently. If you type 'afni_vcheck' you can see what version of the suite you have and what is the latest one available. To update afni, simply use the same wget command as above. This should take much less time than the initial download.
    4. If you plan to use the Talairach atlas that comes with AFNI, you need to download those files separately. You can find then here (afni home) or here (brainmapping ftp). Download files TTatlas+tlrc*, unzip them (only one needs unzipping) and move them to /usr/local/bin/afni/.
    5. Read this only if you absolutely do not want to use wget (it might be a pain to set up but after that - it is soo easy...) - you can also get AFNI the old fashioned way (tar files and all). Instructions and links can be found at 'How to Get AFNI' page.
  4. AIR
    1. Download AIR*-type2.pkg.sit file (from folder 'Tools' on ftp.brainmapping.org ) and install. This will install all of AIR tools in /usr/local/bin/AIR*
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  5. xds
    1. Download xds.pkg.sit file (from folder 'Tools' on ftp.brainmapping.org ) and install. This will install xds tools in /usr/local/bin/xds
    2. Add the path in your .tcshrc file. If you copied the example .tcshrc file from 'RC Files' folder, this path is already included.
  6. UCLATools
    1. UCLATools*.pkg.sit - all of the command line tools as a package. Use this if you are installing the tools for the first time. All of the tools will be installed in /usr/local/bin/UCLATools. You don't need to download this one every time there is an update. Just find the corresponding binary in the list and download it.
    2. Individual tools (binaries) - this is useful for updates (see the top of the ftp page, or the UpdateHistory.html file for notes about recent updates). To download a file you will need to right-click and then select 'download link to disk' (if you just left-click it will try to open a file in the browser and that is no good). Save the file in a convenient place, and then move to /usr/local/bin/UCLATools/ (you will have to do this using the terminal - unfortunately the protected files are not visible in finder).
  7. MATLAB and SPM
    1. MathWorks released MATLAB version 13 that can run under OS X. If you have the install CDs, and the licence - that's it. Install it and it's ready to go. Once you have MATLAB up and running, SPM should be easy to install. Unfortunately as I don't use SPM, I have not tried this (yet?) so I cannot offer any help. However, SPM website might offer some insight on how to accomplish this.