my neuroimaging software install notes for mac OS X mountain lion and ubuntu 12.04 (mostly with neurodebian)

installNotes-neuroImagingSoftware-notaScriptDoNotRun.sh

# [email protected]
# updated: 20130508
#
# These are my personal notes about installing neuroimaging software
# on Mac OS X Mountain/Lion and Ubuntu 12.04 (mostly neurodebian). 
#
# Some of this can be pasted into install scripts or the bash prompt.
# Be careful: this is an active working document, probably filled with errors.
#
# software covered:
#
# - neurodebian virtualm machine
# - itksnap
# - mricron
# - mricrogl
# - imagej/fiji
# - fsl
# - afni
# - BXH/XCEDE tools (from FBIRN)
# - freesurfer
# - spm
# 


###########################
#   Neurodebian VM
###########################

1) Download the neurodebian VM .ova
- http://neuro.debian.net/ -> Get Neurodebian
- Select operating system: Mac or Windows
- Download the .ova or zip file

2) Download and install virtualbox

3) Follow neurodebian install instructions:
written: http://neuro.debian.net/vm.html#chap-vm
video: http://www.youtube.com/watch?v=eqfjKV5XaTE

4) Boot up. Don't bother to select any new packages from the point-and-click wizard that autoruns.

5) Use apt-get to install the software packages listed below


###########################
#   ITK-SNAP
###########################

#-----------------------------------------------------------------
# Installing the ITK-SNAP binary on OS X Mountain/Lion:
# -----------------------------------------------------------------

# Download latest version from the ITK-SNAP Downloads page:
#      http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.Downloads
#      click on  "MacOS Binary (Intel, 64 bit, OSX 10.5+)"
# Drag the ITK-SNAP.app to /Applications folder


# -----------------------------------------------------------------
#  Install the ITK-SNAP binary on Ubuntu 12.04:
# -----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install itksnap



###########################
#   MRIcron
###########################

#-----------------------------------------------------------------
# Installing MRIcron on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# Download latest from http://www.nitrc.org/projects/mricron
# ( probably called "MRIcron [month]/[year] osx.zip")
# Unzip the downloaded file (which currrentlyproduces a folder called osx).
# Install: 
cd ~/Downloads/osx/
mv mricron.app dcm2niigui.app npm.app /Applications/
# Move dcm2nii to a folder in the $PATH, e.g., /usr/local/bin :
echo ${PATH}   # does this contain /usr/local/bin ?
ls /usr/local  # is there a folder called bin inside of /usr/local ? If not: sudo mkdir /usr/local/bin
sudo mv ~/Downloads/osx/dcm2nii /usr/local/bin/


#-----------------------------------------------------------------
# Installing MRIcron on Ubuntu 12.04:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install mricron mricron-data mricron-doc

# remember that preferences are stored here if you would like to edit them:
# ~/.dcm2niigui/dcm2niigui.ini
# ~/.dcm2nii/dcm2nii.ini



###########################
#   MRIcroGL
###########################

#-----------------------------------------------------------------
# Installing MRIcroGL on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# Download from http://www.mccauslandcenter.sc.edu/mricrogl/
# pay attention to downloaded filename: if you already had osx.zip
# in your Downloads folder from mricrON, this may get called "osx(1).zip" etc.
cd ~/Downloads
mkdir mricrogl
cd mricrogl
unzip ~/Downloads/osx.zip
sudo mv mricrogl.app /Applications/
mv *.nii.gz /Users/Shared/sampleBrainVolumes/mricrogl # or other parent of sample data
# save the pdf manual somewhere



###########################
#   ImageJ / FIJI
########################### 

#-----------------------------------------------------------------
# Installing FIJI on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# download dmg file from http://fiji.sc/Downloads, then do this:
cd ~/Downloads
open fiji-macosx.dmg
cp -R /Volumes/Fiji/Fiji.app /Applications/
hdiutil unmount /Volumes/Fiji
open /Applications/Fiji.app 

# then install imagej plugins (instructions below)


#-----------------------------------------------------------------
# Installing ImageJ/FIJI on Ubuntu 12.04:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install fiji

# then install imagej plugins (instructions below)


#-----------------------------------------------------------------
# Installing ImageJ plugins:
#-----------------------------------------------------------------

# Even in 2013 imagej/fiji can't open .nii.gz files without a plugin (though .nii's work).
# Download and install the plugin from http://rsb.info.nih.gov/ij/plugins/nifti.html :
cd ~/Downloads
curl -O http://rsb.info.nih.gov/ij/plugins/download/jars/nifti_io.jar
cp nifti_io.jar /Applications/Fiji.app/plugins/      # ...for OS X . Adapt for linux.

# Re-open imagej/fiji. Opening nii.gz files should now work (drag & drop, or File->Open).
# Also should now see five new commands in imagej/fiji:  
#     File/Import/NIfTI-Analyze, 
#     File/Save As/Analyze (NIfTI-1), 
#     File/Save As/NIfTI-1, 
#     File/Save As/Analyze 7.5 and 
#     Analyze/Tools/Coordinate Viewer.



###########################
#   FSL
###########################

#-----------------------------------------------------------------
# Installing FSL on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# Before installing FSL, freesurfer, or  AFNI on Mountain/Lion be sure to install XQuartz, 
# and logout and then back in: (http://xquartz.macosforge.org)
 
# Google "FSL install" and follow instructions. Currently here:
# http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX#Downloading_the_install_file_without_installing_the_software

# There are multiple ways to install (as of May 2013). I get mixed results with the recommended fslinstaller.py, but I typically use it and then just fix whatever didn't work.

# Run FSL's installer script in  "download only" mode (about 1-hr):
cd ~/Downloads
python fslinstaller.py -o

# Calculate the md5 sum of the downloaded file and use it to launch installation:
fslDownload=fsl-5.0.2.2-macosx.tar.gz
fslDestDir="/usr/local"
fslMD5=`md5 ${fslDownload} | awk '{ print $NF}'` 
python fslinstaller.py -d ${fslDestDir} -f ${fslDownload} -C ${fslMD5}

# After the install completes, confirm that the file /etc/bashrc received a block of FSL environmental variables (below). 
# If not, the install program may have added it to your personal ~/.profile or ~/.bash_profile instead.
# For system-wide installation, remove from those files and append to /etc/bashrc:

#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):

editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER 
# added some FSL setup:
FSLDIR=/usr/local/fsl
PATH=\${FSLDIR}/bin:\${PATH}
export FSLDIR PATH
. \${FSLDIR}/etc/fslconf/fsl.sh
#------------------------------------------
EOF

cat /etc/bashrc 
 
# Either log out and back in again, or issue this terminal command:
. /etc/bashrc

# TEST: did $FSLDIR get exported correctly? This should return "/usr/local/fsl" (no quotes) :
echo $FSLDIR

# TEST: Does fslview exist in /Applications?
ls /Applications
# ...if not create a shortcut like this:
sudo ln -s /usr/local/fsl/bin/fslview.app /Applications/fslview.app

# TEST: we should be able to open /Applications/fslview.app :
open /Applications/fslview.app

# TEST: we should be able to open fslview.app from the commandline :
fslview ${FSLDIR}/data/standard/MNI152_T1_2mm_LR-masked.nii.gz


#-----------------------------------------------------------------
# Installing FSL on Ubuntu 12.04:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install fsl-complete fsl-feeds
# ...but previous to fsl-completed, you needed to apt-get instal fsl-atlases fsl-feeds fsl-first-data fslview and fsl-feeds?
# then get instructions for environmental variables (e.g., may need to source AFNI/FSL script from /etc/bash.bashrc)
man fsl

#-----------------------------------------------------------------
# Installing FSL on Debian 7.0 Wheezy Neurodebian VM:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install fsl-complete fsl-feeds
# ...but previous to fsl-completed, you needed to apt-get instal fsl-atlases fsl-feeds fsl-first-data fslview and fsl-feeds?
# then get instructions for environmental variables (e.g., may need to source AFNI/FSL script from /etc/bash.bashrc)
man fsl

# After the install completes, confirm that the file /etc/bash.bashrc received a block of FSL environmental variables (below). 
# If not, the install program may have added it to your personal ~/.profile or ~/.bash_profile instead.
# For system-wide installation, remove from those files and append to /etc/bash.bashrc:

#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):

editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bash.bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER 
# added some FSL setup:
. /etc/fsl/5.0/fsl.sh
#------------------------------------------
EOF

cat /etc/bashrc 

#-----------------------------------------------------------------
# Install and run FSL test suite ("FEEDS"):
#-----------------------------------------------------------------

# Download FEEDS from FSL (> 270 MB): http://fsl.fmrib.ox.ac.uk/fsldownloads/
# (on neurodebian download via command "sudo apt-get install fsl-feeds")

# Run FEEDS (http://fsl.fmrib.ox.ac.uk/fsl/feeds/doc/):
# (on neurodebian, this is all replaced by command fsl-selftest or /usr/bin/time fsl-selftest)
# 2013 i7 imac: 971.77 real 951.78 user 22.83 sys
cd ~/Downloads (or where ever you saved your download)
tar -zxvf fsl-*-feeds.tar.gz
cd feeds
/usr/bin/time ./RUN all



###########################
#   AFNI
###########################

#-----------------------------------------------------------------
# Installing AFNI on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# Before installing FSL, freesurfer, or  AFNI on Mountain/Lion be sure to install XQuartz, 
# and logout and then back in: (http://xquartz.macosforge.org)

# …then download latest AFNI for Mac, unzip, and move to a reasonable location: 
cd ~/Downloads
curl -O http://afni.nimh.nih.gov/pub/dist/tgz/macosx_10.7_Intel_64.tgz
tar -zxvf macosx_10.7_Intel_64.tgz
sudo mv macosx_10.7_Intel_64 /usr/local/abin

# Add AFNI's new location to the path in /etc/bashrc :
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):
#
editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER  
# added some AFNI environmental variables:
export PATH=/usr/local/abin:\${PATH}
export AFNI_ENFORCE_ASPECT=YES
#------------------------------------------
EOF

cat /etc/bashrc

# Either log out and back in again, or issue this terminal command:
. /etc/bashrc 

# TEST: Open a new terminal window and test your afni install by issuing the command "afni" (no quotes) to open GUI 
# make sure AFNI_ENFORCE_ASPECT is working effectively (see below)


#-----------------------------------------------------------------
# Installing AFNI on Ubuntu 12.04:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install afni afni-atlases
# ...then "man afni" to get instructions for environmental variables
# (e.g., may need to source AFNI/FSL script from /etc/bash.bashrc)

# In the event that the neurodebian version of AFNI is broken/old/whatever
# you may want to substitute a binary version from outside of neurodebian.
# Two steps to do that:
# 1) Download,  unzip, and move to a reasonable destination (not overwriting
# neurodebian's afni in the process):
curl -O http://afni.nimh.nih.gov/pub/dist/tgz/linux_xorg7_64.tgz  # (> 600 MB)
tar -zxvf linux_xorg7_64.tgz
mv linux_xorg7_64 ~/abin
# 2) Kill neurodebian's AFNI environmental variables and add
# this new directory (~/abin in my example) to $PATH (see below)


#-----------------------------------------------------------------
# Installing AFNI on Debian 7.0 Wheezy Neurodebian VM:
#-----------------------------------------------------------------

# I'm currently happy with the version in the neurodebian repos:
sudo apt-get install afni afni-atlases
# ...then "man afni" to get instructions for environmental variables
# (e.g., may need to source AFNI/FSL script from /etc/bash.bashrc)

# For system-wide install, source the AFNI config file from /etc/afni/afni.sh :
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):
#
editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bash.bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER  
# added some AFNI environmental variables:
. /etc/afni/afni.sh
#------------------------------------------
EOF

cat /etc/bashrc


#-----------------------------------------------------------------
# Checking and Setting env variable AFNI_ENFORCE_ASPECT :
#-----------------------------------------------------------------

# In some environments the AFNI GUI allows you to accidentally distort image 
# aspect ratio by resizing an image window. Not good, but avoidable:

# First here's a reminder of how to read and set AFNI environmental variables:
afni -help | grep Vname
afni -help | grep Dname

# If the following command returns no output, the variable AFNI_ENFORCE_ASPECT isn't set
# [sic: yes, this command should end with "=" as written here:]
afni -VAFNI_ENFORCE_ASPECT= 

# To set AFNI_ENFORCE_ASPECT on a per-execution basis, can launch the afni GUI with:
afni -DAFNI_ENFORCE_ASPECT=YES


#-----------------------------------------------------------------
# Unsetting AFNI environmental variables:
#-----------------------------------------------------------------

# Sometimes you need to clear AFNI-related environmental variables, for example 
# if Neurodebian is installed but you need to temporarily use AFNI installed in a user-space directory:
unset `env | awk -F= '/AFNI/ ${print $1}' | xargs`

# ...this would probably be followed by listing your local user-space afni directory 
# earlier in the path than the system-wide afni directory, for example:
export PATH=~/abin:${PATH}

# ...and then check that the "right" AFNI will run:
which afni
which 3dinfo



###########################
#  BXH/XCEDE FBIRN TOOLS
###########################

#-----------------------------------------------------------------
# Installing BXH/XCEDE tools on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# As of May 2013, the shipping binaries of BXH/XCEDE tools includes broken imagemagick.
# Here's a script describing the problem and my work-around: 
# http://goo.gl/9Rd6V

# ...after executing the steps in that script do this to confirm
# the changes to /etc/bashrc :
cat /etc/bashrc 
 
# Either log out and back in again, or issue this terminal command:
. /etc/bashrc

# TEST: did $BXHDIR get exported correctly? This should return a listing of bxh programs :
ls $BXHDIR

#-----------------------------------------------------------------
# Installing BXH/XCEDE tools on Debian Linux 7.0 Wheezy Neurodebian VM
#-----------------------------------------------------------------

# manualy download most recent bxh/xcede release from nitrc: http://www.nitrc.org/projects/bxh_xcede_tools
# ls -l ~/Downloads/bxh_xcede_tools-*.tgz
bxh_xcede_tools-1.10.7-lsb31.i386.tgz
 
#  unpack and install bxh/xcede:
#
# ...first declare the bxh version as it appears in the download filename:
bxhVersion=1.10.7
# ...then unpack and install
cd ~/Downloads
tar -zxvf bxh_xcede_tools-${bxhVersion}-lsb31.i386.tgz
sudo mv bxh_xcede_tools-${bxhVersion}-lsb31.i386 /opt/
sudo ln -s /opt/bxh_xcede_tools-${bxhVersion}-lsb31.i386 /opt/bxh

# for system-wide access, configure the environment via /etc/bashrc :
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):
 
editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bash.bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER 
# added some BXH/XCEDE environment statements:
BXHDIR=/opt/bxh
PATH=\${BXHDIR}/bin:\${PATH}
export BXHDIR PATH
#------------------------------------------
EOF




###########################
#  FreeSurfer
#  WARNINING: Stable 5.2 release WITHDRAWN awaiting upcoming version 5.3
###########################

# If you haven't done so already, obtain a license, and copy the .license file to your 
# $FREESURFER_HOME directory per https://surfer.nmr.mgh.harvard.edu/registration.html


#-----------------------------------------------------------------
# Installing FreeSurfer on Mac OS X Mountain/Lion:
#-----------------------------------------------------------------

# Before installing freesurfer on Mountain/Lion be sure to install XQuartz (http://xquartz.macosforge.org)
# and FSL (b/c FS's install will detect location of FSL).

# Download latest .dmg from the Freesurfer Wiki: 
# http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
# This can be done from the commandline instead of the webpage:
fsFtpDir="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0"
fsFtpFilename="freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg"
cd ~/Downloads
curl -O ${fsFtpDir}/${fsFtpFilename}

# …and to resume a failed download:
curl -C - -o ${fsFtpFilename} ${fsFtpDir}/${fsFtpFilename}

# confirm that the download is valid:
sh <<EOF
curl -s -o freesurfer_md5sums.txt http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt
echo ""
echo "expected md5 sum:"
grep ${fsFtpFilename} freesurfer_md5sums.txt
echo ""
echo "md5sum of downloaded ${fsFtpFilename}:"
md5 ${fsFtpFilename}
echo ""
echo "(re-download if they don't match)"
echo ""
EOF
 
# Doubleclick on the .dmg and run the .pkg installation file found inside of it.  
# Detailed instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/Installation 
# (Note the folder that this installs to, likely /Applications/freesurfer, which you will assign to $FREESURFER_HOME below.)

# add post-install config to /etc/bashrc per the bash section of 
# http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration) :
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):
#
editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a /etc/bashrc >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER   
# added some freesurfer environmental variables:
export FREESURFER_HOME=/Applications/freesurfer
. \${FREESURFER_HOME}/SetUpFreeSurfer.sh
#------------------------------------------
EOF

cat /etc/bashrc 

# copy the sample data to a place where users can write to it:
cp -a $SUBJECTS_DIR /Users/Shared/fs_sampleSubjects
# edit ${FREESURFER_HOME}/SetUpFreeSurfer.sh to reflect the change in $SUBJECTS_DIR, then
# either log out and back in again, or issue this terminal command:
. /etc/bashrc 
 
# TEST: open a new terminal windows. You should see a number of freesurfer-related
# lines at the top of the new terminal window, and all the terminal windows you open after that.

# TESTS: Test your installation by issuing the test commands detailed on the Testing Freesurfer webpage 
# (as of January 2013: http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer )

# TEST freeview:
freeview \
-v $SUBJECTS_DIR/bert/mri/norm.mgz \
-v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow \
-f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow \
-f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red \
-f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red

# TEST tkmedit (volume viewer):
tkmedit bert orig.mgz
tkmedit bert norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

# TEST tksurfer (surface viewer):
tksurfer bert rh pial 

# TEST short reconstruction segment (< 30 minutes)
recon-all -s bert -autorecon1 

# TEST full reconstruction (~ 24 hours)
# 2013 i7 iMac:
#     recon-all -s bert finished without error at Mon May  6 00:52:13 EDT 2013
#     22032.75 real     21947.85 user        60.84 sys
recon-all -s bert -all 


#-----------------------------------------------------------------
# Installing FreeSurfer on Ubuntu 12.04 :
#-----------------------------------------------------------------

# download latest .tar.gz from the Freesurfer Wiki: 
# http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
# This can also be done from the commandline instead of the webpage:
fsFtpDir="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0"
fsFtpFilename="freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0.tar.gz"
cd ~/Downloads
wget ${fsFtpDir}/${fsFtpFilename}
 
# …and to resume a failed download:
curl -C - -o ${fsFtpFilename} ${fsFtpDir}/${fsFtpFilename}
 
# confirm that the download is valid:
sh <<EOF
curl -s -o freesurfer_md5sums.txt http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt
echo ""
echo "expected md5 sum:"
grep ${fsFtpFilename} freesurfer_md5sums.txt
echo ""
echo "md5sum of downloaded ${fsFtpFilename}:"
md5 ${fsFtpFilename}
echo ""
echo "(re-download if they don't match)"
echo ""
EOF



###########################
#   SPM (Mountain Lion)
###########################

# Download the latest SPM 8 package.
# (currently from http://www.fil.ion.ucl.ac.uk/spm/software/spm8/ )

# Unzip the downloaded SPM package and move the resulting SPM folder to /usr/local , 
# so that SPM's program files are not in /usr/local/spm.

# Open matlab and issue the command "userpath;" (no quotes). This will tell you what
# folder Matlab is going to look in for certain files. You care about this folder because 
# in the next step you're going to create a special file that gets placed there.

# In the Matlab window issue the command "pathtool;" (no quotes). This opens a new window. 
# In this window, add /usr/local/spm to # the list of folders that Matlab searches for files. 
# Upon clicking "save", this window may complain about problems creating a file called pathdef.m, and ask you where you would like to put this file. Put it on the folder that was returned by the userpath # command you entered earlier.

# Test your installation by closing and then reopening Matlab. Type "spm;" (no quotes) at the Matlab prompt, and the SPM graphical user interface should open.