Beauchamp:Software Installation

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(Updating AFNI)
(Updating AFNI)
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   rm -r {$pkg}.tgz {$pkg}
   rm -r {$pkg}.tgz {$pkg}
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If AFNI won't run after updating, it is probably because some of your libraries are out of date. Follow the instructions on the AFNI web site to install all necessary libraries; this will install the newest versions. If errors still occur, a failsafe method is to compile AFNI on your machine; this will ensure that only the available libraries are used.
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If AFNI won't run after updating, it is probably because some of your libraries are out of date. The easiest fix is to first try adding the following line to your .cshrc file that directs to the right library path (solution found from [http://afni.nimh.nih.gov/afni/community/board/read.php?1,135117,135194#msg-135194 this] AFNI message board thread). This will help if you get an error after running 3dSkullStrip and are running a non "noglib" version of AFNI.
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Alternatively, an easier fix may be to add the following line to your .cshrc file that directs to the right library path (solution found from [http://afni.nimh.nih.gov/afni/community/board/read.php?1,135117,135194#msg-135194 this] AFNI message board thread).
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  setenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin
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setenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin
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where $HOME/abin is the directory you keep AFNI (ex: Applications/AFNI).
where $HOME/abin is the directory you keep AFNI (ex: Applications/AFNI).
 +
 +
If this still does not help, follow the instructions on the AFNI web site to install all necessary libraries; this will install the newest versions. If errors still occur, a failsafe method is to compile AFNI on your machine; this will ensure that only the available libraries are used.
Some statistical programs in AFNI require the free statistical package "R". This can be downloaded from
Some statistical programs in AFNI require the free statistical package "R". This can be downloaded from

Revision as of 09:29, 10 September 2013

Brain picture
Beauchamp Lab



Contents

Computer Problems

If you have having software or hardware problems, submit a help ticket describing the problem. Do not be afraid to request help from MSIT. They are paid to help you! The link for help tickets is http://med.uth.tmc.edu/msit/mshelp.htm For installing software, you will need to get administrator privileges. Use Directory Utility to set the superuser password (see http://support.apple.com/kb/HT1528 for details). Then reboot, try to login as user "root". This same password can then be used in X11 sudo.

Backing Up

Because hard disks fail, it is important to back up your files regularly. The best way to back up files on your Mac is automatically, using Time Machine. First, open a Terminal window. Copy and paste this command into terminal (all on one line):

 defaults write com.apple.systempreferences TMShowUnsupportedNetworkVolumes 1

Mount the servers (msnbafmri and ike). Select one of the data drives as a Time Machine destination. Currently, we are using data1 on ike. For extra important files, you can also use a thumbdrive, an external hard drive, the UT NAS, or DropBox. One issue with Time Machine network backup is whether TM does an incremental backup (fast) or a full backup every time (slow). See these sites for discussion http://www.somelifeblog.com/2009/02/fixed-time-machine-backup-to-network.html http://en.wikipedia.org/wiki/Time_Machine_(software) http://rolf.haynberg.de/?p=83

If you have parallels installed on your computer, you can tell Parallels (under the Preferences menu) not to back up the Parallels VM. This will save time because there is no real reason to back up Windows (can be easily reinstalled).

Setting up a New Mac Computer

After MSIT has plugged in your spiffy new computer and completed the basic installations (Office, Outlook, etc), there are a few more steps to make sure everything is ready to go to analyze some awesome data. First you will need to make sure you have admin privileges on your computer so that you have the necessary permissions to install new software.

XCode and Terminal

The first thing you need to do is download XCode from the App Store. An account on the Apple Store is required (MSB has one) but the download is free. You must also go to Preferences/Downloads in XCode and install the command line utilities.

Next you need to configure your terminal. Go to Applications > Utilities and drag Terminal to the dock as you will most likely be using it often. Open terminal and go to Preferences. Under "Shells open with", click "Command (complete path)" and enter:

  /bin/tcsh

Then you will need to copy over a .cshrc file which will help you set up your path every time you open Terminal. To copy over Michaels, enter in the command line

  cp /Volumes/data9/surfaces/scripts/.cshrc ~/

If at any point you need to add something to your path, open the .cshrc file

  open -e ~/.cshrc

and add it in the following line:

  set path = ( $path /sw/bin /Applications/AFNI/ /Applications/MATLAB_R2011a.app/bin)

Fink/AFNI/Freesurfer

Next you will need to download Fink. You can do so here:

  http://www.finkproject.org/download/srcdist.php

Follow the instructions on the page. For 10.8.1, you will have to install Java first. Every time the install guide asks you a question, the default answer will be in square brackets (i.e. [1]) or capitalized (i.e [Y/n]). Choose the default options unless you know what you're doing. After installation is complete, run the pathsetup command listed in the instructions and then run:

  fink selfupdate-rsync
  fink index -f

To get the necessary packages for AFNI, run:

  fink install glib2-dev netpbm openmotif3 wget

Next you will need to download AFNI. If you are running OS X Lion, it's best to get the version with no glib (true as of 01/2012).

  http://afni.nimh.nih.gov/pub/dist/tgz/macosx_10.6_Intel_64.no.glib.tgz

After you have expanded it, rename the folder afni and move it over to Applications. It is important to NOT update your AFNI for now (true as of 2/2012). This will override the no glib version. Eventually this will be fixed, but for now stick with the no glib.

Next you will download FreeSurfer.

  https://surfer.nmr.mgh.harvard.edu/fswiki/Download

This takes about 30 minutes to download. Go grab some coffee. After it finishes downloading and installing, if your .cshrc file doesn't already have it (to check, type: open -e ~/.cshrc), add FreeSurfer to the path:

  echo ‘setenv FREESURFER_HOME /Applications/freesurfer‘ >> ~/.cshrc
  echo ‘source $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc

You'll also want to download XQuartz here:

  http://xquartz.macosforge.org/trac/wiki

Setting up Mendeley

To help us share PDFs we use Mendeley + a shared Dropbox folder.

  1. Assuming you have a dropbox account, ask a lab member to share the folder "LabReferences" with you
  2. Go to http://www.mendeley.com, setup an account, and download/install the software

Once you have downloaded and installed Mendeley, we need to add a "watch folder" to Mendeley

  1. Open Mendeley
  2. File -> Watch Folder
  3. Navigate the file tree to Dropbox and check the LabReferences box
  4. Select OK

If you want to have your own copy of the PDFs (for annotations, etc), we need to setup Mendeley to organize your library into another directory

  1. Mendeley Dekstop -> Preferences
  2. Choose the File Organizer Tab
  3. Check the box for Organize my files and select an appropriate directory
  4. You may also check the boxes for "Sort files into subfolders" and "Rename document files" to have Mendeley create a more structured file hierarchy

When you have a PDF that you would like to share, simply copy it to the LabReferences/ folder in your Dropbox. Because all Mendeleys are watching that folder, it will be imported to everyone's library automatically.

NB: If people have setup their Mendeley to organize files into a separate directory, once you copy a file into LabReferences, you may not be able to "take it back."

Additional Software

For additional software you might like (Adobe Illustrator, EndNote, Parallels, etc), check the Installing Software section. If we don't have a valid license number anymore we may need to purchase a new one.

It is also a good idea to set up TimeMachine on your computer to backup everything to the Data 1 server. If you have Parallels already installed, go to TimeMachine > Options and exclude that folder from the backup.

Installing software

ISOs and General Information

ISOs (CD or DVD disk images) are kept on the server in

 /data1/Software_isos

Open the ISO of the software that you would like to install; if a license key is required, it will typically be in a separate .txt file. MSIT (Ismael Perez) will install a basic set of software, including Microsoft Office, if asked. Ismael can also give you the address from which the software can be downloaded. At one point, the URL for Office was

 \\139.52.5.233\nba-tera\office 2007
 \\139.52.5.233\NBA-Tera\Office2010

In January 2013, it was

 Smb://ms-nba2.uthouston.edu/MacSoftware

In July 2012, the product key was MGFF3-V43J4-CRW33-PD9GF-J6TGK. MSIT requires security settings, such as automatic logout after 10 minutes. VirusScan can be downloaded from the MSIT web site, currently at

 http://its.uth.tmc.edu/resources_mcafeedownload.htm

If it is to be used for experiments, these security features can be a problem. MSIT will disable them if an exception form is filled out. If the PC is to be used for experiments, install Presentation software. The XVid CODEC is preferred; Virtual Dub and Audigy software are useful free editing tools.

 http://www.xvid.org

The VLC video player is useful

 http://www.videolan.org/

Also FFDShow

 http://sourceforge.net/projects/ffdshow

If you are running Windows on a Mac via BootCamp in order to run Presentation, you may find it easier to swap the control and Command keys for consistency with Mac OSX. In Windows XP, This can be done with

 remapkey.exe 

A program that is in the Windows Server 2003 Resource Kit Tools (free download from Microsoft). Download the tools, go to Start/Run/remapkey Drag the "Left Windows" key onto the "Ctrl" key and vice-versa. This edits the registry and takes effect on the next reboot. The registry can also be edited manually. If you find the Windows Startup and Shutdown sounds annoying they can be turned off from Control Panel/Sounds (in Windows XP). In Windows 7, remapkey.exe does not work. Instead, edit registry manually or try one of the following utilities: KeyTweak (in "FullTeach" mode); SharpKeys, KeyMapper, etc.

For software installation, it can be useful to be a "root" (super-user). To enable this function, type

 sudo passwd root

Enter your admin password, then a new password for root, and you're done

That Startup "beep" made by the Mac can be disable with various utilities, including

 StartupSoundPrefPane

ISOs can be created using the Disk Utility in Mac OSX.

Installing Octave and Psychtoolbox

These instructions were tested under Mac OSX 10.7.4 with Octave 3.2.6 and Psychtoolbox (PTB) 3.0. They should be completed AFTER the initial UNIX installation steps, including installing XCode tools, including command line tools; this installs "svn" which is needed. The instructions require access to ms-nbafmri, so make sure you are connected to the network via ethernet, UTHSC wifi, or have an open VPN connection

  1. Install Octave-3.2.3-i386.dmg from ms-nbafmri/data/SoftwareISOs (i.e., double-click the dmg file)
    1. Optional: In the Extras/ directory of the Octave dmg there is Gnuplot, which is necessary if you want to make quick plots with Octave
  2. Copy DownloadPsychtoolbox.m from ms-nbafmri/data/SoftwareISOs to the desktop
  3. Open Octave (default install is /Applications/Octave), cd to the desktop, and execute the Download script
 octave-3.2.3:1> cd Desktop/
 octave-3.2.3:2> DownloadPsychtoolbox
  1. Accept all certificate requests and choose defaults during installation
  2. Ensure PTB is installed correctly by testing a demo:
 octave-3.2.3:3> LoadMovieIntoTexturesDemoOSX

If you get an error at this step, it may be because PTB doesn't like your dual monitor configuration. Exit Octave, Change Display Mode to "Mirrored", then Open Octave and run the demo again

Happy PTB'ing!!

† If you try to plot from Octave ( plot( 1:10) ) and get an error about DYLD_LIBRARY_PATH, then we need to make one more edit for plotting to work:

 sudo open -e /Applications/Gnuplot.app/Contents/Resources/bin/gnuplot

Find the line: DYLD_LIBRARY_PATH="${ROOT}/lib:${DYLD_LIBRARY_PATH}" and replace it with DYLD_LIBRARY_PATH="${ROOT}/lib" Save the file then relaunch Octave and try to plot again

  octave-3.2.3:1> sombrero()

Installing Matlab

If you want to use Psychtoolbox with Matlab (and who wouldn't?) a 32-bit version is needed; R2010a was the last 32-bit release. R2010 a located in the SoftwareISOs folder on the server. Follow the instructions in the UT_License.rtf file. for Intel 32-bit OSX will do the trick) as well. For newer versions:

  1. Download and install matlab here. Get login name and pw from Mike
  2. Currently, we use the NBA Computational Core license. To access this license, place the following in the network.lic file in the licenses subdirectory:
 SERVER ms-nba2.ms.uthouston.edu INTERNET=129.106.154.4
 USE_SERVER

January 2009: A common cause for failure is that the DNS service cannot interpret the hostname. Instead, us

 SERVER 1129.106.154.4 INTERNET=129.106.154.4 27000
 USE_SERVER

The last "27000" is probably optional. Another cause for failure is that you have downloaded the latest version of Matlab from Mathworks, while our license only supports a previous version. For instance, in Jan 2009, our license only support 2008a, although the website encourages you to download 2008b as the latest version.

Presentation

How to get

Download from NeuroBehavioral Systems website (http://www.neurobs.com/) Trial license is free and good for 30 days. Student version is $100 good for 1 year. You will need to place the order first and then fax/email them both sides of your student ID along with the order and invoice number, as well as the name and contact of your academic advisor. You will need to make an account first to be able to order. After you have successfully purchased the license, you must sign in under the lab ID to retrieve the access code.

Using two monitors

- In the Windows display settings (right click on Desktop --> Properties --> Settings), choose the second monitor and select "Extend my Windows desktop onto this monitor"

- Restart Presentation, then go to Settings --> Video and add another display (bottom of page) and choose the appropriate driver for each (top of the page)

- Make sure the second monitor (the one that will show the stimulus) is selected as the primary display device.

Getting Help

In addition to the software Help, and looking at previous codes written in the lab, questions may be asked from NeuroBehavioral systems by posting them on their forum. Usually they are very responsive and helpful. Other users may also post a response to your question.

Audio Setup

From Settings-->Audio Choose Custom Mixer-->Primary Buffer Otherwise there will be a ~20ms delay between the time of auditory stimulus presentation and the time that the voltage actually gets to the audio jack! This would be specially crucial for TMS experiments. If you get an error when trying to play audio stimuli (something like "Device Is In Use") there is probably a strange interaction with Parallels. This can be fixed in Parallels 7 by Virtual Machine/Configure/Sharing select all sharing options (Share Profile and SmartMount)


Response Button affecting Parallel Port

Make sure you set the response_port_output header parameter to false, otherwise whenever for example response button 3 in pressed, binary code of 3 (00000011) will be sent to the parallel port! In SDL section, before begin type:

response_port_output =  false;

Configuring Presentation to use USB for output

Attaching USB to the computer The computer first needs the NI-DAQmx software installed - download NI USB-6501 (http://zone.ni.com/devzone/cda/tut/p/id/6913). Before you install anything, make sure you have .NET Framework 2.0 installed (available at: http://www.microsoft.com/downloads/details.aspx?FamilyID=0856EACB-4362-4B0D-8EDD-AAB15C5E04F5&displaylang=en). Under the installer features menu, the bare minimum is:

NI-DAQmx 8.8.0
 ->.NET Framework 3.5 Lanugages
 ->.NET Framework 2.0 Lanugages
 ->.NET Framework 1.1 Lanugages
 ->ANSI C Support

You will have to restart after you install the software.

After the restart, connecting the device via USB, Windows will detect a "New Data Acquisition Device", and present you with a window offering several options. Select "Configure and Test This Device Using NI Measurement & Automation Explorer" and run a Self-Test when the window opens. If this passes, the USB device can now be used to control TMS through Presentation.

Configuring Presentation to use USB

Now we need to make a few adjustments to the settings. Under the 'Settings' tab, select the 'Port' option and find the 'Output Ports' box. In this box we need to have a total of 2 ports.

Add the first port, and make sure the following options are set:

Port: USB-6501
Data source: port0
Register span: 1
Inversion mask: 0
Default pulse width: 5 ms

For the second port, the following options need to be set:

Port: USB-6501
Data source: port1
Register span: 1
Inversion mask: 255
Default pulse width: 5 ms

Using Presentation via USB The USB controller uses a new library Image:Beauchamp USB TMS library.pcl to control the TMS machine. A sample presentation you can use to test to the USB control of the TMS is available: Image:Beauchamp OhmanTMSScenario.sce. In this scenario, the up/down arrows are used to control the intensity of the TMS, while the space bar is used to toggle arming/disarming the device, and the return key is used to fire the device. The sample presentation can also be used to help write code in the future - perhaps the most important point is that it is no longer necessary to define an output port inside the pcl, including the Beauchamp_USB_TMS_library.pcl is sufficient.

Using and recording sound responses

Sound response buttons can be defined in Presentation using Settings-->Response-->Devices-->sound device (threshold or offset)

Once you chose "sound device" click on "properties" button to the left of "Devices" window and adjust the parameters. You need to choose the correct microphone from the pull down menu, set the threshold, ...

To record a sound response, check the "save responses" button and set the recording duration. Each response will be saved in a separate wave file. You can also check the button to save all responses in one wave file (in addition to the individual wave files).

Another way to record sounds is using:

sound_recording{
duration = 1000;
base_filename = "some_file_name";
};

within a trial.

Parallels and Presentation

Presentation runs only under Windows, but can be run on a Mac using BootCamp OR virtualization software such as VMWare or Parallels. Here are some benchmarks for a 2010 MacBook Pro with a 2.66 GHz Intel Core i7 and 4 GB RAM:

To assess performance under Windows 7, go to Control Panel/Performance Information and Tools.


Scores are on a scale from 1.0 to 7.9

 calculations per second     memory access    Windows graphics    3D graphics for games   hard drive

Windows 7 (boot camp) 6.8 5.5 6.4 6.4 5.9

windows 7 (parallels) (1 CPU, 1GB RAM) 4.9 4.5 5.9 4.8 6.2

windows 7 (parallels) (2 CPU, 2GB RAM) 4.9 5.5 5.9 4.8 6.2

To summarize, biggest hit is calculations per second and graphics.

Running Windows on a Mac

It can be useful to have Windows installed on a Mac. There are a number of ways to do this. Parallels can be purchased; this allows Windows to be used at the same time as Mac OSX. The free Boot Camp utility that comes with Mac OSX can be used but in this configuration, only one of OSX or Windows can be used at a time. In either case, a licensed copy of Windows must be available. For Parallels, download and install Parallels. Select "Install Windows from a Disk Image". Go to

 ms-nbafmri:\data\SoftwareISOs\windows7.cdr

Select "Does not need product key" and continue with installation. AFTER installation, start Windows, go to Control Panel, All Control Panel Items, System, scroll down, click on "Enter new Product Key", copy and paste product key

 6WJJY-XXMJW-YXJXW-FD6HX-6G3XB

WinSCP

WinSCP is a useful program that allows you to connect from Windows to our servers. This is especially helpful when transferring over a subject's files after scanning them. The program can be downloaded here:

http://winscp.net/eng/download.php

To set up the login session, go to Stored Sessions > New. File protocol is SFTP, then enter the appropriate username and password for the server. Host name is the server address.

Configuring a New Mac Server

Notes on 2012 Mac Mini Server The name of the new Mac Mini server is ms-nbafmri To connect, type Apple-K, then

 afp://139.52.4.123

The username is beauchamplab


Older Notes


Special boot-up key strokes (hold down during boot-up): Apple-Option-P-R to erase the PRAM; C to boot up from CD; Option for a list of all boot-up choices, including CD, BootCamp, etc.

New servers can be ordered with two hard drives. These hard drives can be set to mirror one another so that if one fails, the server can continue operating. To do this, boot the Server from the OSX DVD that came with the Server (using the Startup Disk icon in System Preferences.) Then, use Disk Utility to drag and drop the Server hard drives into a RAID set. Finally, reinstall OSX on the new RAID set. Apple recommends creating an image of the boot-up disk onto an external disk using the Image utility. Then, in the event of a hard disk crash the Server can quickly and easily be restored to health, including all configurations. Before reformatting the hard disk, use the disk utility Repair Disc and Repair Permission options. Ask Network Ops (David Zhang) for fixed IP addresses for the server. Currently, servers are located in the NBA VLAN #236. Network Ops needs the MAC addresses for each jack. The MAC address can be read from the rear of the machine or as follows:

 ifconfig

returns

  ether 00:17:f2:06:7b:04

Cabling guys (David Findlay) need to know the Mac address and the VLAN. Current <ac addresses for new XServe (ike) are

en0 00:24:36:f2:b6:e0
en1 00:24:36:f2:b6:dc

with corresponding DHCP

129.106.236.182
129.106.236.183

The HP Tape Loader has Mac address: 002264CCE364 to IP address 129.106.236.185

Bidwell has Mac address 00:0d:93:9e:73:92 to IP address

 129.106.236.182


In general, no extra software (AFNI, etc.) is installed on Servers to ease maintenance and allow them to be devoted to their calling. The Promise RAID can be configured through the serial port-to-RJ11 cable included with the system. It may be possible to do this with the XServe (possibly using the "screen" command in Terminal or a terminal emulation program such as Zterm) but I could not figure out how to connect. Instead, a PC laptop with a serial cable and Microsoft Hyperterminal (C:/Program Files/WindowsNT/hypertrm.exe) was used. For more details, see Beauchamp:PromiseConfig After initial configuration, the RAID can be tweaked via the web interface. Or, through it's web-based management system. The system will automatically obtain an IP address from DHCP. It will broadcast this address via Bonjour. Open Safari, open Preferences/Bookmarks, click "Include Bonjour". Click Bonjour on favorites toolbar and select VTrak. Current IP address is 139.52.6.21. Log in is administrator, password is password. (Computer running Safari must be on same subnet.) To setup the Promise RAID, follow the instructions on http://support.apple.com/kb/HT1164 and http://support.apple.com/kb/HT1200 Which essentially means using the web interface (Adminstrative Tools/Import/Configuration Script) to upload this text file; it is then executed automatically. Image:Beauchamp PromiseRAIDConfigScript.txt Also note that there are many different fiber channel cards and cables. See the compatibility matrix at

 http://support.apple.com/kb/HT1769

Creating and synchronizing takes many hours (overnight). After creation of the RAID set, turn on the XServe. You will see an error message saying the disks are not readable. Use Disk Utility to partition the drives (one big partition for each RAID set). Next, use WorkGroup Manager to add users with passwords who can access the drives. To ease managment, separate groups can be created for each partition (e.g. data1 group, data2 group). Users who want access to a particular partition can be easily added or subtracted to the group. Under the Sharing tab of Server Admin, each partition can be given an owner (MSB) and a group (e.g. data1), both of which have Read & Write access. Under the File Sharing tab, click on a Volume to share, then click Share. It will show up in the Share Points section. AppleCare recommends creating a separate folder to share if it will be used for Time Machine backups, to avoid creating share points within share points. Use RAID admin to check on the RAID. A helpful guide is the Mac OSX File Services Administrator manual.

Setting up user accounts. Create accounts for each user (easiest if use same username and ID as on previous system). It is easiest to create one "group" for each RAID set (data drive). Then users can be easily added to groups to give them access to the appropriate data. This is done in Workgroup Manager. Then, new users


Notes on a New Mac Server

Apple no longer makes the XServe, so must switch to NAS/SAN, or a PC server, or a Mac Pro or Mac Mini. possibilities:

  1. Drobo ordered a demo unit, couldn't get it to work
  2. Mac Mini with thunderbolt + Promise thunderbolt 6-bay RAID (daisy chain 2 for 12-bay)
  3. ReadyNAS
  4. SATA Beast http://www.nexsan.com/products/satabeast-xi/index.aspx#/gallery
  5. Promise RAID http://store.apple.com/us/product/H1142VC/A?mco=MTY3ODQ5OTY
  6. Promise Thunderbolt to connect to Mac Mini
  7. G-Tech RAID (small) http://store.apple.com/us/product/H4656VC/A?mco=MTY3ODQ5OTY
  8. Aberdeen RAID (recommended by Ismael) http://www.aberdeeninc.com
  9. Synology NAS http://www.synology.com/

Installing/Updating Programs

XCode/XTools

See "Configuring a new Mac", above, for info on installing XCode.

http://trac.macosforge.org/projects/xquartz

1. XcodeTools and X11SDK from the Leopard DVD. 2. Maybe the latest X11 package from trac.macosforge.org 3. glib2-dev glib netpbm openmotif from fink (stable source will do). 4. mesa mesa-libglw mesa-libglw-shlibs mesa-shlibs from fink (unstable source).

If you have an older Mac, you will periodically need to go to Apple.com and download the latest XCode and XTools. They are NOT automatically installed by the Apple Software Update routines.

"You will need to re-install this package after future OS, and Security Updates delivered through Apple's Software Update. Additionally, you should reinstall this package after installing XCode."

From: http://xquartz.macosforge.org/trac/wiki/X112.6.1

Configuring your login shell

UNIX can use different command line interfaces, called shells. The shell preferred by AFNI and FreeSurfer is called tcsh. The UNIX command line can be accessed through either the X11 program or the Terminal program. The Terminal program is preferred; it makes cutting and pasting between windows and changing window properties easier. To change the login shell used by Terminal, go to Terminal/Preferences/Startup, in "Shells open with" select Command and enter

 /bin/tcsh

For ease of access, drag the Terminal icon (or the X11 icon) to the dock.

Changing the login shell used by X11 is more complex.


Every time tcsh starts, it reads commands from the file .cshrc To copy MSB's tcsh, type

 cp /Volumes/data9/surfaces/scripts/.cshrc ~/

Because AFNI uses all three mouse buttons, you must tell the Mac to allow this. Click on system preferences/Mouse and Keyboard/Mouse and select the middle mouse button to be button #3 and the right mouse button to be button #2. You may also have to go to system preferences and turn off the middle mouse button to access Dashboard/Expose/Spaces.

Other software that may be handy to have: Adobe Creative Suite; Firefox; Skype

To install software, it may be necessary to have a root password. To create one, type sudo passwd root


NB: SUMA is unstable with some versions of X11. If SUMA crashes, upgrade your X11 as follows. First see which is the latest version by going to

   http://xquartz.macosforge.org/trac/wiki/Releases

Next, follow these instructions (replacing 2.3.0.pkg with the latest version)

 quit X11
 http://xquartz.macosforge.org/downloads/X11-2.3.0.pkg
 Install the new X11
 logout, login and relaunch X11


The built-in Preview software in Mac OSX is the best way to view PDFs and does not require downloading anything (unlike Adobe Acrobat). For editing PDFs, the free Skim software is recommended http://skim-app.sourceforge.net/


Fink

This step may not be required for newer Macs.

Fink is a program package manager for Macs. Download the program from the Fink webpage:

http://fink.sourceforge.net/.

The program in the dmg file will be straightforward. You can copy finkcommander to the applications folder for a GUI interface. You should update your libraries every few weeks by running the following: fink selfupdate; fink update-all

To add it to your path, add source /sw/bin/init.csh To your .cshrc file.

Installing Required Libraries for AFNI

Type the following line to have Fink grab the newest versions:

fink install glib2-dev glib netpbm openmotif3
fink install wget

If you’re using OS X Lion you may not need the glib package.


AFNI

If AFNI is being installed for the first time, it must be downloaded manually from

 http://afni.nimh.nih.gov/afni/download/afni/releases/latest

Click and download whatever the latest (newest) distribution is for Intel Macs. After downloading, double click the tar file; this will create a new directory containing all of the AFNI programs. Drag this folder into the Applications directory. For ease of access, rename the folder and call it "afni" (easier to type than, for example, macosx_10.5_Intel). If you are updating, delete the old afni folder before renaming.

AFNI uses all three mouse button. Therefore, you must have a 3-button mouse. SUMA uses the function keys. To make them easier to use, go to the Mac OS keyboard menu and click on the checkbox next to "Use all F1 keys as standard function keys". SUMA also uses Ctrl-Arrow keys for functions. To make this key combination easier, go to the Mac OS keyboard/keyboard shortcuts menu and un-click any checkboxes that use Ctrl-arrow keys (or change them to a different key combination).

The distribution for newer Macs includes the graphics libraries needed by SUMA. This means you can skip the step in the AFNI install web page about installing these. However, you may need to add the following command to your .cshrc file

  setenv DYLD_FALLBACK_LIBRARY_PATH /Applications/AFNI

Updating AFNI

AFNI is frequently updated, so it is important to make sure you have the most recent version. To update, type

 @update.afni.binaries -defaults

Many common problems arise because users are using an old version of afni. Type to find out what version you have. If it is older than one month, update it!

 afni -version

An older less-automatic way to update (for Intel Macs) is the following. Set the variable "pkg" to the latest version:

 set pkg = macosx_10.5_Intel_64
 wget http://afni.nimh.nih.gov/pub/dist/tgz/{$pkg}.tgz
 tar xvfz {$pkg}.tgz

No matter how you update, you must type

 rehash

after you update so that the shell will find the newest version or programs.

Another way (change the package and bindir appropriately):

sudo @update.afni.binaries -package macosx_10.5_Intel_64 -bindir /Applications/afni

Optionally, it can be good to test the new version BEFORE overwriting the old version. Here is how we can test SUMA:

 cd {$pkg}
 ./suma

If it works, we copy it over the old version (type "which afni" if you are not sure which directory afni is in)

 mv {$pkg}/* /Applications/AFNI/
 rm -r {$pkg}.tgz {$pkg}

If AFNI won't run after updating, it is probably because some of your libraries are out of date. The easiest fix is to first try adding the following line to your .cshrc file that directs to the right library path (solution found from this AFNI message board thread). This will help if you get an error after running 3dSkullStrip and are running a non "noglib" version of AFNI.

 setenv DYLD_FALLBACK_LIBRARY_PATH $HOME/abin

where $HOME/abin is the directory you keep AFNI (ex: Applications/AFNI).

If this still does not help, follow the instructions on the AFNI web site to install all necessary libraries; this will install the newest versions. If errors still occur, a failsafe method is to compile AFNI on your machine; this will ensure that only the available libraries are used.

Some statistical programs in AFNI require the free statistical package "R". This can be downloaded from

http://www.biometrics.mtu.edu/CRAN/bin/macosx/

FreeSurfer

FreeSurfer is another set of programs developed at NIH for the analysis of functional neuroimaging. We mainly use it for cortical surface reconstruction. Their download page is part of an extensive wiki that describes its many functions.

https://surfer.nmr.mgh.harvard.edu/fswiki/Download

Updates to the software are normally posted on the listserv. To set the correct paths for Freesurfer paste the following lines into a terminal window:

echo ‘setenv FREESURFER_HOME /Applications/freesurfer‘ >> ~/.cshrc
echo ‘source $FREESURFER_HOME/SetUpFreeSurfer.csh' >> ~/.cshrc

FreeSurfer needs a license file. You can request on their web site or copy it. Copy it FROM the SoftwareISOs directory into the directory where you have installed FreeSurfer:

 cd /Volumes/data/SoftwareISOs
 cp FreeSurferLicenseFile /Applications/freesurfer/.license

Caret

Go to Caret's Download Webpage, register for an account, and download the newest release. Copy the caret folder to the Applications folder on your machine and add the following line to your .cshrc file:

  set path = ($path /Applications/caret/bin/)


OsiriX

OsiriX is a DICOM viewer that may be helpful if you need to upload DICOMs, especially from a CT scan taken after electrode surgery with epilepsy patients. It can be downloaded from here:

  http://www.osirix-viewer.com/


R

This program is used for the structural equation modeling. If you plan on doing functional connectivity as part of your data analysis, this is a good program to have. You can download it here:

  http://cran.r-project.org/bin/macosx/

To utilize 1dSEM, click the R icon on the console, then locate the 1dSEM.R script in the AFNI folder and load it.

Creating Symbolic Links

It is useful to have symbolic links from the command line so you do not need to type the full path to a file. The program ln creates such symbolic links. Here are a couple of examples:

ln –s /Volumes/data9/surfaces/ /surfaces
ln –s /Volumes/data1/UT /UT

The paths are now linked to /surfaces/ and /UT/.


Printing

Printing Double Sided

On a new computer you may notice that the option to print two-sided is greyed out. To fix this, go to System Preferences, Print & Scan, select the printer, then press the Options & Supplies button. Under the Driver tab, click Duplex Printing Unit.

Dell 5100cn Color Laser Printer

The printer IP is 139.52.6.205 To see the current status of the printer go to http://139.52.6.205 Here is a copy of the manual http://openwetware.org/images/8/83/Dell_5100cn.pdf

To use the printer, download the current drivers for your computer from the Dell website

 http://support.dell.com/support/downloads

Shortcut: drivers are on the server in

 /data/SoftwareISOs/MiscSoftware/Dell_5100_cn

On Windows XP, you must first add a port, then configure the printer. On Mac OSX, first run the Installer. Then open System Preferences/Print & Fax Click the "+" button to add a printer, click on "IP" and enter the IP address (above.)

    • Protocol must be Line Printer Daemon -- LPD


There are sometimes several drivers to choose from. The PS (postscript) driver under Windows cannot collate. The PCL driver does. So if you need to collate, use the PCL driver.

In Windows, you must add a Port with this address, then install the correct printer driver and tell it to print to the port. On the Mac, go to System Preferences, Print & Fax, Click the +, Click IP, enter the IP into the address field.

HP Photosmart Color Inkjet Printer

Insert the installation CD into your computer and follow the instructions. The Mac installation software is in /Volumes/data9/Software_isos/HPPrinter/HP Installer The status of the printer can be checked at

 http://hpfd76cd.local./index.htm?cat=info&page=printerInfo

Mounting Volumes

Mounting RAID Volumes from Windows

You must have a Mac with a valid user account. On the Mac, go to System Preferences, Sharing, and enable Windows Sharing. The menu should say

 Windows users can access your computer at \\XXX.XXX.XXX.XXX\YYY

For Mac OSX 10.5, go to System Preference, Sharing. Enable File Sharing. Click the "+" button and add your user to the list of Users; change permissions to be Read & Write. Click on Options and Enable "SMB" which is what Windows uses. Click the user name (you will be prompted for your password).

You may also need to able your user account. Look for the message

 Enabled accounts: Ashley Kingon

If your account is not enabled, click on the "Accounts" button and enable it.

Additional steps for Windows VISTA:

Go to the the Start menu and choose 'Computer'

Go to Computer: Local Disk (C:): Windows: regedit

After clicking on the registry editor application:

 Go to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Lsa
 Click on LmCompatibilityLevel
 Set value to 1
 Restart computer

In Windows, go to Internet Explorer and type in the URL above.

Mounting a Volume after sshing to a different machine

For example. I ssh onto tellmore machine. Now I want to access data9 from his machine.

in my home directory (~) (on tellmore) I make a directory called mount, inside of mount I make a directory called data9 (or which ever volume I am mounting), then I mount data9.

cd ~
mkdir mount
cd mount
mkdir data9
mount_afp -i afp://akingon@129.106.236.180/data9 data9
enter password 

and now you can cd into data9

Python

Path:

import sys
sys.path # this will show the current path settings
sys.path.append('C:\new_path') # this will add the new path, however only until the 
                               # current python session is open

To more permanently add a path, use the Windows environment variable PYTHONPATH

Control Panel --> System --> Advanced tab --> Environment Variables (Bottom of page)--> System variables --> look for PYTHONPATH, if it does not exist, use NEW to create it. Use semi-colon to add multiple paths:

C:\path1;C:\path2

IDLE (Python's GUI editor) is slow!

Displaying outputs on IDLE makes the loop very slow. Here is a test:

import time
t0 = time.clock()
counter = 0
while time.clock() <= t0 + 1:
    print "junk"
    counter += 1

Running this code on my 2GHz laptop, results in < 400 Hz loop rate using IDLE. Whereas rate is as high as 15 KHz if the code is run from the command line (by double clicking on the python file).

This is very important when detecting a fast event. For example reading parallel port to detect the TTL pulse from MRI scanner [the philips 3T scanner's pulse is currently only 75 microseconds long].

Misc Unix Notes

Loops in tcsh are a handy way to automate data processing. Here is an un-commented example. The syntax varies from shell to shell.

set sdall = ( X Y Z P O R T Y)
set idx = 1
foreach ec (FL FM FN FQ FS FU FW FY FZ)
set sd = $sdall[$idx]
@ idx++
echo $idx
end

Here is a while loop for tcsh

 set idx = 1
 while ($idx < 10)
 @ idx++
 echo $idx
end
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