initial commit

mne_data/MNE-sample-data/subjects/fsaverage/mri.2mm/README

@@ -0,0 +1,140 @@
+
+fsaverage/mri.2mm
+
+These are volumes sampled into a 2mm space. The primary purpose of
+these is to support volume-based fMRI analysis as performed in
+FS-FAST. This 2mm space is the space that is used by default in
+FS-FAST to perform "talairach" group analysis (ie, in the mni305
+space). The raw functional data are sampled into this space when
+preproc-sess is run with the -mni305 flag. When a group analysis is
+done, the output space will be this 2mm space. It is possible to use a
+1mm space, but this can create huge files.
+
+These files can be used to render the statistical results on a volume
+(though this is not really necessary as they can be rendered directly
+on the 1mm volumes). Also, the aseg.mgz created can be used to
+generate labels/masks of subcortical structures directly in the group
+average space. These can be used with mri_volcluster.
+
+These files were created with the following commands:
+
+# Resample each of these volumes using trilin
+foreach vol (orig brain brainmask mni305.cor T1)
+  mri_vol2vol --mov ../mri/$vol.mgz --s fsaverage --tal \
+  --o $vol.mgz --no-save-reg
+end
+
+# Resample the aseg 
+mri_label2vol --seg ../mri/aseg.mgz --temp orig.mgz \
+  --regheader ../mri/orig.mgz --o aseg.mgz
+
+Note: we don't want to do aparc+aseg because the surface-based 
+labels should really be used in a surface-based analysis.
+
+# checks
+tkmedit -f T1.mgz -aux brain.mgz -seg ./aseg.mgz
+tkregister2 --mov ./orig.mgz --s fsaverage --regheader --reg junk
+
+#-----------------------------------------------------------
+
+Creation of subcortical mask. A challenge for doing analyses in three
+ROIs (left hemi, righ hemi, subcortical) is making the ROIs mutally
+exclusive while not excluding any voxels. This is particularly hard in
+this analysis because a cortical voxel in one subject can map to a
+subcortical voxel in another when using the transform to MNI305
+space. 
+
+A map of the subcortical structures for each of the buckner 40 where
+mapped into the mni305 2mm space. A probability map was then
+created. This was repeated for the cortical ribbon and for cerebellum
+by itself. 
+
+1. An initial mask was created taking voxels with any 
+subcortical origins in the native space as long as they had fewer than
+80% cortex. 
+
+2. Cerebellum is a special case because it is so close to fusiform
+that it is easy to get bleed over. For this case, a mask was made of
+any cerebellum voxels that had at least 20% cortex. Any voxels in this
+mask were then excluded from the mask from step 1 to create a new
+mask.
+
+3. Little islands were excluded by running connected components and
+taking the largest cluster. 
+
+4. This mask was then dialted by one voxel then eroded by one voxel to
+remove holes and make the final mask less jagged.
+
+
+# ----- Below For Version 5 --------------------#
+Everything above is for 5.1 and higher.
+
+The mask is created based on mri/subcort.prob.mgz which was created
+with make_average_subcort. subcort.prob.mgz is the raw probability of
+a voxel being in a subcortical gray matter structure based on the
+Buckner40. Inevitably, this mask will include more than just
+subcortial gray matter structures, but we would rather have the mask
+be too big than too small.
+
+# Resample into 2mm space
+mri_vol2vol --mov ../mri/subcort.prob.mgz \
+  --s fsaverage --tal --o subcort.prob.mgz \
+  --no-save-reg
+
+Threshold at .05 (meaning that at least 5% of the subjects at 
+a voxel must have a subcortical label). Also dilate by 2 to
+expand the mask.
+
+mri_binarize --i subcort.prob.mgz --min .05 \
+  --dilate 2 --o subcort.mask2.mgz
+
+Erode by 1. The net result of dilating by 2 then eroding
+by 1 is that holes are filled in and the edges are 
+a little smoother.
+
+mri_binarize --i subcort.mask2.mgz --min .5 \
+  --erode 1 --o subcort.mask.mgz
+
+rm subcort.mask2.mgz
+
+#-----------------------------------------------------------
+
+Creation of registration matrix between the 2mm fsaverage/mni305 space
+and the 2mm mni152 space. This can be used to convert data in the 2mm
+fsaverage/mni305 space into the mni152 2mm space.
+
+set d = $SUBJECTS_DIR/fsaverage
+
+# Create registration matrix between the full 256^3, 1mm3 
+# volume and the 2mm space (simple regheader)
+tkregister2 --mov $d/mri.2mm/brain.mgz --targ $d/mri/brain.mgz \
+  --regheader --reg $d/mri.2mm/reg.2mm.dat --noedit
+
+# Registration between the fsaverage/mni305 subject (full 256^3, 1mm3)
+# and the 2mm mni152 space.  This was created by hand.
+# $FREESURFER_HOME/average/mni152.register.dat 
+
+# Compute the registration between the 2mm fsaverage space and the
+# mni152 2mm space by concatenating the two matrices above.
+mri_matrix_multiply -im $d/mri.2mm/reg.2mm.dat \
+  -iim $FREESURFER_HOME/average/mni152.register.dat \
+  -om $d/mri.2mm/reg.2mm.mni152.dat
+
+# Check the registration
+tkregister2 --mov $d/mri.2mm/brain.mgz \
+  --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
+   --reg $d/mri.2mm/reg.2mm.mni152.dat
+
+# To view without reslicing
+tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
+  -overlay sig.nii -reg reg.2mm.mni152.dat
+
+# To do the conversion/reslicing, run something like
+mri_vol2vol --mov sig.nii --reg reg.2mm.mni152.dat \
+  --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
+  --o sig.mni152.nii
+
+# To view with reslicing
+tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
+  -overlay sig.mni152.nii
+

mne_data/MNE-sample-data/subjects/fsaverage/mri.2mm/reg.2mm.dat

@@ -0,0 +1,9 @@
+fsaverage
+2.000000
+2.000000
+0.150000
+1.000000e+00 0.000000e+00 0.000000e+00 2.000000e+00 
+0.000000e+00 1.000000e+00 0.000000e+00 1.600000e+01 
+0.000000e+00 0.000000e+00 1.000000e+00 -9.000000e+00 
+0 0 0 1
+round

mne_data/MNE-sample-data/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat

@@ -0,0 +1,9 @@
+subject-unknown
+1.000000
+1.000000
+0.150000
+1.002140 -0.017676 -0.007170 0.592940
+-0.014581 0.002707 -0.998974 -2.468433
+0.012895 1.002740 -0.009373 8.678564
+0.000000 0.000000 0.000000 1.000000
+round

mne_data/MNE-sample-data/subjects/fsaverage/mri/transforms/reg.mni152.2mm.dat

@@ -0,0 +1,9 @@
+fsaverage
+1.000000
+1.000000
+0.150000
+9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 
+-1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 
+-1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 
+0 0 0 1
+tkregister

mne_data/MNE-sample-data/subjects/fsaverage/mri/transforms/talairach.xfm

@@ -0,0 +1,7 @@
+MNI Transform File
+
+Transform_Type = Linear;
+Linear_Transform =
+1.0 0.0 0.0 0.0 
+0.0 1.0 0.0 0.0 
+0.0 0.0 1.0 0.0;

mne_data/MNE-sample-data/subjects/fsaverage/scripts/build-stamp.txt

@@ -0,0 +1 @@
+freesurfer-x86_64-redhat-linux-gnu-dev4-20090216

mne_data/MNE-sample-data/subjects/fsaverage/scripts/csurfdir

@@ -0,0 +1 @@
+/usr/local/freesurfer/stable5

mne_data/MNE-sample-data/subjects/fsaverage/scripts/recon-all.cmd

@@ -0,0 +1,10 @@
+#-----------------------------------------
+#@# Cortical Parc 2 lh Thu Dec 30 17:40:05 EST 2010
+
+ mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 
+
+#-----------------------------------------
+#@# Cortical Parc 2 rh Thu Dec 30 17:40:58 EST 2010
+
+ mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 fsaverage rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot 
+

mne_data/MNE-sample-data/subjects/fsaverage/scripts/recon-all.done

@@ -0,0 +1,10 @@
+------------------------------
+SUBJECT fsaverage
+DATE Thu Dec 30 17:41:50 EST 2010
+USER nicks
+HOST terrier
+PROCESSOR x86_64
+OS Linux
+Linux terrier 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
+$Id: recon-all,v 1.313.2.32 2010/12/30 19:11:13 nicks Exp $
+/usr/local/freesurfer/stable5/bin/recon-all

mne_data/MNE-sample-data/subjects/fsaverage/scripts/recon-all.env

@@ -0,0 +1,129 @@
+Thu Dec 30 17:40:00 EST 2010
+FREESURFER_HOME /usr/local/freesurfer/stable5
+Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5
+/autofs/cluster/freesurfer/subjects/fsaverage
+setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
+-s fsaverage -cortparc2
+Linux terrier 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
+
+cputime      unlimited
+filesize     unlimited
+datasize     unlimited
+stacksize    10240 kbytes
+coredumpsize 0 kbytes
+memoryuse    unlimited
+vmemoryuse   unlimited
+descriptors  1024 
+memorylocked 32 kbytes
+maxproc      201728 
+
+SSH_AGENT_PID=6065
+HOSTNAME=terrier
+HOST=terrier
+TERM=xterm
+SHELL=/usr/local/bin/tcsh
+QTDIR=/usr/lib64/qt-3.3
+QTINC=/usr/lib64/qt-3.3/include
+PATHSET=1
+GROUP=nicks
+USER=nicks
+LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:*.dmg=01;31:
+OPENWINHOME=/usr/openwin
+HOSTTYPE=x86_64-linux
+SSH_AUTH_SOCK=/tmp/ssh-ntSizn6022/agent.6022
+KDEDIR=/usr
+USERNAME=nicks
+HELPPATH=/usr/openwin/lib/help
+MAIL=/var/spool/mail/nicks
+PATH=/usr/pubsw/packages/AFNI/current/bin:/usr/local/freesurfer/stable5/bin:/usr/local/freesurfer/stable5/fsfast/bin:/usr/pubsw/packages/fsl/current/bin:/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin:/usr/pubsw/packages/valgrind/current/bin:/usr/local/cula/bin64/:/usr/local/cuda/bin/:/autofs/space/terrier_001/users/nicks/freesurfer/bin:/autofs/space/terrier_001/users/nicks/freesurfer/fsfast/bin:/usr/pubsw/packages/fsl/current/bin:/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin:/usr/pubsw/packages/tcltktixblt/current/bin/:/usr/pubsw/packages/cmake/current/bin:/homes/11/nicks/bin:/homes/11/nicks/bin/sloc_count:/usr/bin:/usr/local/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/java/current/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/pubsw/bin:/usr/pubsw/packages/caret/current/bin
+DESKTOP_SESSION=default
+GDM_XSERVER_LOCATION=local
+INPUTRC=/etc/inputrc
+PWD=/autofs/cluster/freesurfer/subjects/fsaverage
+XMODIFIERS=@im=none
+KDE_IS_PRELINKED=1
+LANG=C
+GDMSESSION=default
+SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
+SHLVL=3
+HOME=/homes/11/nicks
+OSTYPE=linux
+VENDOR=unknown
+MACHTYPE=x86_64
+LOGNAME=nicks
+QTLIB=/usr/lib64/qt-3.3/lib
+DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-1wHKW0nOde,guid=41a48c9649d362b9c441d3004d1a4b3d
+LESSOPEN=|/usr/bin/lesspipe.sh %s
+DISPLAY=:0.0
+G_BROKEN_FILENAMES=1
+XAUTHORITY=/tmp/.gdmD4GNOV
+GTK_RC_FILES=/etc/gtk/gtkrc:/homes/11/nicks/.gtkrc-1.2-gnome2
+SESSION_MANAGER=local/terrier:/tmp/.ICE-unix/6104
+GNOME_KEYRING_SOCKET=/tmp/keyring-nMAWKq/socket
+GNOME_DESKTOP_SESSION_ID=Default
+DESKTOP_STARTUP_ID=
+COLORTERM=gnome-terminal
+WINDOWID=26341869
+PRINTER=deca
+LPDEST=deca
+EDITOR=emacs
+TERRIER_HOME=/autofs/space/terrier_001/users/nicks
+TERRIER_SD=/autofs/space/terrier_002/users/nicks/subjects
+TINIA_HOME=/autofs/space/tinia_001/users/nicks
+MINERVA_HOME=/autofs/space/minerva_001/users/nicks
+BLADE_HOME=/autofs/space/blade_005/users/nicks
+JC_HOME=/autofs/space/jc_001/users/nicks
+HADES_HOME=/autofs/space/hades_001/users/nicks
+HYDRA_HOME=/local_mount/space/hydra/1/users/nicks
+STORM_HOME=/Users/Shared
+SLEET_HOME=/Users/nicks
+MIST_HOME=/Users/Shared
+ASPASIA_HOME=/Users/Shared/nicks
+RAIN_HOME=/Users/nicks
+FISHIE_HOME=/home/nicks
+ASTERIX_HOME=/autofs/space/asterix_001/users/nicks
+PKGS_ROOT=/autofs/space/terrier_001/users/nicks/pkgs
+SUBJECTS_DIR=/autofs/cluster/freesurfer/subjects
+LD_LIBRARY_PATH=/usr/pubsw/packages/valgrind/current/lib:/usr/local/cula/lib64:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/pubsw/packages/cppunit/current/lib
+CMAKE_HOME=/usr/pubsw/packages/cmake/current
+CVSROOT=/space/repo/1/dev
+SVNMNEROOT=/space/orsay/8/users/msh/SVN-MNE/trunk
+MNE_ROOT=/usr/pubsw/packages/mne/current
+MATLAB_ROOT=/usr/pubsw/packages/matlab/current
+FREESURFER_HOME=/usr/local/freesurfer/stable5
+FSDEV=/autofs/space/terrier_001/users/nicks/dev
+FSSTABLE=/autofs/space/terrier_001/users/nicks/stable5/dev
+FUNCTIONALS_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/sessions
+OS=Linux
+FS_OVERRIDE=0
+FSFAST_HOME=/usr/local/freesurfer/stable5/fsfast
+MINC_BIN_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin
+MNI_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni
+MINC_LIB_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib
+MNI_DATAPATH=/autofs/space/terrier_001/users/nicks/freesurfer/mni/data
+FSL_DIR=/usr/pubsw/packages/fsl/current
+LOCAL_DIR=/usr/local/freesurfer/stable5/local
+FSF_OUTPUT_FORMAT=nii
+FMRI_ANALYSIS_DIR=/usr/local/freesurfer/stable5/fsfast
+MNI_PERL5LIB=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib/perl5/5.8.5
+PERL5LIB=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib/perl5/5.8.5
+FSLDIR=/usr/pubsw/packages/fsl/current
+FSL_BIN=/usr/pubsw/packages/fsl/current/bin
+FSLOUTPUTTYPE=NIFTI_GZ
+FSLMULTIFILEQUIT=TRUE
+FSLTCLSH=/usr/pubsw/packages/fsl/current/bin/fsltclsh
+FSLWISH=/usr/pubsw/packages/fsl/current/bin/fslwish
+FSLLOCKDIR=
+FSLMACHINELIST=
+FSLREMOTECALL=
+FSLCONFDIR=/usr/pubsw/packages/fsl/current/config
+FSLMACHTYPE=linux_64-gcc4.1
+FSLDISPLAY=/usr/bin/display
+FSLCONVERT=/usr/bin/convert
+FIX_VERTEX_AREA=
+NVIDIA_CUDA_SDK=/usr/local/cuda/sdk
+CARET_HOME=/usr/pubsw/packages/caret/current
+SET_TCL_VARS=1
+MRI_UMASK=2
+RECONALL_USAGE_FILE=/space/freesurfer/recon-all_run_log
+REQUIRE_FS_MATCH=0

mne_data/MNE-sample-data/subjects/fsaverage/scripts/recon-all.env.bak

@@ -0,0 +1,129 @@
+Thu Dec 30 17:34:43 EST 2010
+FREESURFER_HOME /usr/local/freesurfer/stable5
+Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/stable5
+/autofs/cluster/freesurfer/subjects/fsaverage
+setenv SUBJECTS_DIR /autofs/cluster/freesurfer/subjects
+-s fsaverage -cortparc
+Linux terrier 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 19:04:48 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
+
+cputime      unlimited
+filesize     unlimited
+datasize     unlimited
+stacksize    10240 kbytes
+coredumpsize 0 kbytes
+memoryuse    unlimited
+vmemoryuse   unlimited
+descriptors  1024 
+memorylocked 32 kbytes
+maxproc      201728 
+
+SSH_AGENT_PID=6065
+HOSTNAME=terrier
+HOST=terrier
+TERM=xterm
+SHELL=/usr/local/bin/tcsh
+QTDIR=/usr/lib64/qt-3.3
+QTINC=/usr/lib64/qt-3.3/include
+PATHSET=1
+GROUP=nicks
+USER=nicks
+LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35:*.dmg=01;31:
+OPENWINHOME=/usr/openwin
+HOSTTYPE=x86_64-linux
+SSH_AUTH_SOCK=/tmp/ssh-ntSizn6022/agent.6022
+KDEDIR=/usr
+USERNAME=nicks
+HELPPATH=/usr/openwin/lib/help
+MAIL=/var/spool/mail/nicks
+PATH=/usr/pubsw/packages/AFNI/current/bin:/usr/local/freesurfer/stable5/bin:/usr/local/freesurfer/stable5/fsfast/bin:/usr/pubsw/packages/fsl/current/bin:/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin:/usr/pubsw/packages/valgrind/current/bin:/usr/local/cula/bin64/:/usr/local/cuda/bin/:/autofs/space/terrier_001/users/nicks/freesurfer/bin:/autofs/space/terrier_001/users/nicks/freesurfer/fsfast/bin:/usr/pubsw/packages/fsl/current/bin:/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin:/usr/pubsw/packages/tcltktixblt/current/bin/:/usr/pubsw/packages/cmake/current/bin:/homes/11/nicks/bin:/homes/11/nicks/bin/sloc_count:/usr/bin:/usr/local/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/java/current/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/pubsw/bin:/usr/pubsw/packages/caret/current/bin
+DESKTOP_SESSION=default
+GDM_XSERVER_LOCATION=local
+INPUTRC=/etc/inputrc
+PWD=/autofs/cluster/freesurfer/subjects/fsaverage
+XMODIFIERS=@im=none
+KDE_IS_PRELINKED=1
+LANG=C
+GDMSESSION=default
+SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
+SHLVL=3
+HOME=/homes/11/nicks
+OSTYPE=linux
+VENDOR=unknown
+MACHTYPE=x86_64
+LOGNAME=nicks
+QTLIB=/usr/lib64/qt-3.3/lib
+DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-1wHKW0nOde,guid=41a48c9649d362b9c441d3004d1a4b3d
+LESSOPEN=|/usr/bin/lesspipe.sh %s
+DISPLAY=:0.0
+G_BROKEN_FILENAMES=1
+XAUTHORITY=/tmp/.gdmD4GNOV
+GTK_RC_FILES=/etc/gtk/gtkrc:/homes/11/nicks/.gtkrc-1.2-gnome2
+SESSION_MANAGER=local/terrier:/tmp/.ICE-unix/6104
+GNOME_KEYRING_SOCKET=/tmp/keyring-nMAWKq/socket
+GNOME_DESKTOP_SESSION_ID=Default
+DESKTOP_STARTUP_ID=
+COLORTERM=gnome-terminal
+WINDOWID=26341869
+PRINTER=deca
+LPDEST=deca
+EDITOR=emacs
+TERRIER_HOME=/autofs/space/terrier_001/users/nicks
+TERRIER_SD=/autofs/space/terrier_002/users/nicks/subjects
+TINIA_HOME=/autofs/space/tinia_001/users/nicks
+MINERVA_HOME=/autofs/space/minerva_001/users/nicks
+BLADE_HOME=/autofs/space/blade_005/users/nicks
+JC_HOME=/autofs/space/jc_001/users/nicks
+HADES_HOME=/autofs/space/hades_001/users/nicks
+HYDRA_HOME=/local_mount/space/hydra/1/users/nicks
+STORM_HOME=/Users/Shared
+SLEET_HOME=/Users/nicks
+MIST_HOME=/Users/Shared
+ASPASIA_HOME=/Users/Shared/nicks
+RAIN_HOME=/Users/nicks
+FISHIE_HOME=/home/nicks
+ASTERIX_HOME=/autofs/space/asterix_001/users/nicks
+PKGS_ROOT=/autofs/space/terrier_001/users/nicks/pkgs
+SUBJECTS_DIR=/autofs/cluster/freesurfer/subjects
+LD_LIBRARY_PATH=/usr/pubsw/packages/valgrind/current/lib:/usr/local/cula/lib64:/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/pubsw/packages/cppunit/current/lib
+CMAKE_HOME=/usr/pubsw/packages/cmake/current
+CVSROOT=/space/repo/1/dev
+SVNMNEROOT=/space/orsay/8/users/msh/SVN-MNE/trunk
+MNE_ROOT=/usr/pubsw/packages/mne/current
+MATLAB_ROOT=/usr/pubsw/packages/matlab/current
+FREESURFER_HOME=/usr/local/freesurfer/stable5
+FSDEV=/autofs/space/terrier_001/users/nicks/dev
+FSSTABLE=/autofs/space/terrier_001/users/nicks/stable5/dev
+FUNCTIONALS_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/sessions
+OS=Linux
+FS_OVERRIDE=0
+FSFAST_HOME=/usr/local/freesurfer/stable5/fsfast
+MINC_BIN_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni/bin
+MNI_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni
+MINC_LIB_DIR=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib
+MNI_DATAPATH=/autofs/space/terrier_001/users/nicks/freesurfer/mni/data
+FSL_DIR=/usr/pubsw/packages/fsl/current
+LOCAL_DIR=/usr/local/freesurfer/stable5/local
+FSF_OUTPUT_FORMAT=nii
+FMRI_ANALYSIS_DIR=/usr/local/freesurfer/stable5/fsfast
+MNI_PERL5LIB=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib/perl5/5.8.5
+PERL5LIB=/autofs/space/terrier_001/users/nicks/freesurfer/mni/lib/perl5/5.8.5
+FSLDIR=/usr/pubsw/packages/fsl/current
+FSL_BIN=/usr/pubsw/packages/fsl/current/bin
+FSLOUTPUTTYPE=NIFTI_GZ
+FSLMULTIFILEQUIT=TRUE
+FSLTCLSH=/usr/pubsw/packages/fsl/current/bin/fsltclsh
+FSLWISH=/usr/pubsw/packages/fsl/current/bin/fslwish
+FSLLOCKDIR=
+FSLMACHINELIST=
+FSLREMOTECALL=
+FSLCONFDIR=/usr/pubsw/packages/fsl/current/config
+FSLMACHTYPE=linux_64-gcc4.1
+FSLDISPLAY=/usr/bin/display
+FSLCONVERT=/usr/bin/convert
+FIX_VERTEX_AREA=
+NVIDIA_CUDA_SDK=/usr/local/cuda/sdk
+CARET_HOME=/usr/pubsw/packages/caret/current
+SET_TCL_VARS=1
+MRI_UMASK=2
+RECONALL_USAGE_FILE=/space/freesurfer/recon-all_run_log
+REQUIRE_FS_MATCH=0