# # This a modified version of the standard .cshrc file for NMR users. # # The commands in this file are executed each time a new csh shell # is started. # # #setenv PRINTER cyclades #setenv LPDEST cyclades #if the color printer should be default, use this # setenv PRINTER admincolor setenv LPDEST admincolor if ( ! $?PATHSET ) then setenv PATHSET 1 set path = ( \ ~/bin \ ~/scripts \ ~/scripts/commands \ ~judith/bin \ ~/bin/linux \ /usr/pubsw/bin \ ~/bin/scripts_studies \ ~/bin/ImgTools/linux \ ~ona/bin/linux \ . \ # ~tldavis/bin/`uname -s`/`uname -r` \ # ~tldavis/bin/`uname -s` \ /usr/bin/X11 \ /autofs/homes/005/judith/bin/scripts_studies/TOOLS_AFNI \ /autofs/homes/005/judith/bin/scripts_studies/TOOLS_matlab \ /autofs/homes/005/judith/bin/scripts_studies/TOOLS_bc \ /autofs/homes/005/judith/bin/scripts_studies/TOOLS_dg \ /autofs/homes/005/judith/bin/scripts_studies/TOOLS \ /usr/pubsw/packages/AFNI/current/bin \ /usr/pubsw/packages/fsl/current/bin \ $path \ ) foreach dir ( /usr/openwin/bin /usr/dt/bin /usr/ccs/bin /opt/SUNWspro/bin ) if ( -d $dir ) then set path = ( $dir $path ) endif end foreach dir ( /usr/bin/X11 /usr/openwin3/bin /usr/ucb ) if ( -d $dir ) then set path = ( $path $dir ) endif end endif # skip remaining setup if not an interactive shell if ($?USER == 0 || $?prompt == 0) exit ##new afni setenv AFNI_PLUGINPATH /usr/pubsw/packages/AFNI/current/bin # /usr/pubsw/packages/AFNI/current/bin \ ## old afni #/usr/devsw/packages/AFNI/bin \ ##DTK alias dtk "/autofs/space/ocean_003/users/software/TrackVis_DTK/dtk/dtk" ##Trackvis alias trackvis "/autofs/space/ocean_003/users/software/TrackVis_DTK/trackvis" #FSL setup setenv FSLDIR /usr/pubsw/packages/fsl/current source $FSLDIR/etc/fslconf/fsl.csh # list directories in columns alias ls 'ls -CFh --color' alias a alias alias h history alias df 'df -k \!*' alias du 'du -k \!*' alias su 'su - \!*' # general aliases for everyday use alias cd 'set old="$cwd"; chdir \!*' alias back 'set back="$old"; set old="$cwd"; cd "$back"; unset back; dirs' alias mv 'mv -i -b' # make mv safe # alias rm 'remove' alias rmold 'rm *~' alias e 'emacs' alias sdraw '/usr/pubsw/packages/openoffice.org/current/program/sdraw' alias scalc '/usr/pubsw/packages/openoffice.org/current/program/scalc' alias display '/usr/bin/display' alias convert '/usr/bin/convert' alias swriter '/usr/pubsw/packages/openoffice.org/current/program/swriter' alias paint '/usr/bin/kolourpaint' alias xds '/homes/5/tldavis/bin/Linux/xds' alias orientationcheck \ 'fslview /autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/fsl/3.3.2/etc/standard/avg152T1.hdr' alias jip '~jbm/bin/jip' alias MRIcro '/autofs/homes/005/judith/bin/scripts_studies/TOOLS/startmricro' alias mat 'matlab7.7 &' alias mat32 'matlab7.7 -glnx86' ## For Freesurfer/FS-FAST stuff alias nmrenv2 source /usr/local/freesurfer/nmr-dev-env alias nmrenv source /usr/local/freesurfer/nmr-std-env alias forfnirt setenv FSL_DIR /usr/pubsw/packages/fsl/4.1.2 ## For MNE Stream setenv NEUROMAG_ROOT /space/orsay/8/megdev/megsw-neuromag alias mne_man 'acroread /space/orsay/8/megdev/megsw/mne/doc/MNE-manual-*.pdf' alias meg 'cd /space/ocean/4/users/MEG' alias neuromag_setup 'setenv NEUROMAG_ROOT /space/orsay/8/megdev/megsw-neuromag' alias mne_setup 'source /space/orsay/8/megdev/megsw/mne/setup/mne/mne_setup_analysis_csh' alias mne_setup_dev 'source /space/orsay/8/megdev/megsw-dev/mne/setup/mne/mne_setup_analysis_csh' alias burn_meg_cd '/space/orsay/8/users/megenv/bin/burn_meg.pl' alias megsd 'setenv SUBJECTS_DIR /space/ocean/4/users/MEG/' alias ss 'setenv SUBJECT ' ## for cvs alias cvs_now 'setenv CVS_RSH ssh' ## For Seder Software alias seder_setup 'source /space/megraid/41/seder/seder_files/programs/helpers/seder_source_me_csh' ## For Matti C code... alias ccode_setup 'setenv SRC_ROOT /space/orsay/8/megdev/msh/' ## For my local versions of stuff alias nmrdaniel 'source ~/scripts/commands/nmrdaniel' alias mnedaniel 'source ~/scripts/commands/mnedaniel' setenv MEG_SCRIPTS ~/MTstudy/MEG/blockDesign/scripts setenv MRI_SCRIPTS ~/MTstudy/studyDir ## For openoffice: alias so '/usr/pubsw/bin/soffice2 &' # Giant list o' aliases: alias NOTES 'cd ~judith/NOTES' alias INDEX 'cd ~judith/INDEX' # alias maps 'cd diffusion/dti/*/cor/m # alias fromt "from | tail -8" # alias wt "setenv IS_WT 1;WTools.x &;unsetenv IS_WT" alias freesurfer-dev "source /usr/local/freesurfer/nmr-dev-env; source ~/bin/afnienv" alias freesurfer-beta "source /usr/local/freesurfer/nmr-stable2-env; source ~/bin/afnienv" alias freesurfer "source /usr/local/freesurfer/nmr-std-env; source ~/bin/afnienv" alias newfsl "setenv FSL_DIR /usr/pubsw/packages/fsl/3.3.2" alias afnienv "source ~/bin/afnienv" #alias tktmp "tkmedit -f /space/structure/1/freediffusion/data/TEMPLATES/avg152T2-bet_000.bfloat " alias tktmp "tkmedit -f /space/ocean/4/users/templates/avg152T2-bet_000.bfloat " # Drives alias stroke "cd /space/stroke/1/users" alias ocean1 "cd /space/ocean/1/users/" alias ocean2 "cd /space/ocean/2/users/" alias ocean3 "cd /space/ocean/3/users/" alias ocean4 "cd /space/ocean/4/users/" alias ocean5 "cd /space/ocean/5/users/" alias ocean6 "cd /space/ocean/6/users/" # Studies alias acu "cd /space/ocean/2/users/ACUPUNCTURE/" alias dex "cd /space/ocean/1/users/DEX/" alias dti "cd /space/ocean/1/users/DEX/DTI_analysis/" alias long "cd /space/invaders/5/stroke/SS_long/" alias cross "cd /space/invaders/5/stroke/SS_cross/" alias dexafni "cd /space/ocean/1/users/DEX_AFNI" alias ID "cd /space/ocean/2/users/ID" alias anat "cd /space/ocean/2/users/ANAT" alias scripts "cd /autofs/homes/005/judith/bin/scripts_studies" alias longafni "cd /space/ocean/1/users/LONG_AFNI" alias acuafni "cd /space/ocean/1/users/ACUPUNCTURE_AFNI" alias controls "cd /space/ocean/4/users/CONTROLS_VF_SM" alias sdti "cd /space/ocean/1/users/DEX/Stroke_DTI" alias cdti "cd /space/ocean/1/users/DEX/Control_DTI" alias DTF "cd /autofs/space/recovery_002/users/DTF_results" # SUMA and AFNI stuff alias dexcontralh 'suma -spec /autofs/space/ocean_002/users/ANAT/DEX/beta/avg_std_surf_S10_flipped_unflipped/avg_std_lh.spec' alias dexcontrarh 'suma -spec /autofs/space/ocean_002/users/ANAT/DEX/beta/avg_std_surf_S10_flipped_unflipped/avg_std_rh.spec' alias sumalh 'suma -spec /space/ocean/2/users/ANAT/SS_long/LONG001_020429_schaechter/SUMA/stdmesh_sm50/MapIco_lh_std.spec -sv /space/ocean/2/users/ANAT/SS_long/LONG001_020429_schaechter/SUMA/LONG001_020429_schaechter_SurfVol+orig' alias sumarh 'suma -spec /space/ocean/2/users/ANAT/SS_long/LONG001_020429_schaechter/SUMA/stdmesh_sm50/MapIco_rh_std.spec -sv /space/ocean/2/users/ANAT/SS_long/LONG001_020429_schaechter/SUMA/LONG001_020429_schaechter_SurfVol+orig' alias dexsumalh 'suma -spec /space/ocean/2/users/ANAT/DEX/beta/avg_std_surf_C10S9_native/avg_std_lh.spec' alias dexsumarh 'suma -spec /space/ocean/2/users/ANAT/DEX/beta/avg_std_surf_C10S9_native/avg_std_rh.spec' alias dexdevsumalh 'suma -spec /space/ocean/2/users/ANAT/DEX/dev/avg_std_surf_C10_S10_native/avg_std_lh.spec' alias dexdevsumarh 'suma -spec /space/ocean/2/users/ANAT/DEX/dev/avg_std_surf_C10_S10_native/avg_std_rh.spec' alias talsumalh 'suma -spec /autofs/space/ocean_002/users/ANAT/ACU/ACU004_030616_bc/SUMA/stdmesh/tal/MapIco_lh_std.spec -sv ACU004_030616_bc_SurfVol+tlrc' alias talsumarh 'suma -spec /autofs/space/ocean_002/users/ANAT/ACU/ACU004_030616_bc/SUMA/stdmesh/tal/MapIco_rh_std.spec -sv ACU004_030616_bc_SurfVol+tlrc' alias talsumalh2 'suma -spec /autofs/space/ocean_002/users/ANAT/DEX/beta/DEX008/SUMA/stdmesh/tal/MapIco_lh_std.spec -sv DEX008_SurfVol+tlrc' alias talsumarh2 'suma -spec /autofs/space/ocean_002/users/ANAT/DEX/beta/DEX008/SUMA/stdmesh/tal/MapIco_rh_std.spec -sv DEX008_SurfVol+tlrc' alias sd 'setenv SUBJECTS_DIR' alias dexsd 'setenv SUBJECTS_DIR /autofs/space/ocean_002/users/ANAT/DEX/beta' alias longsd 'setenv SUBJECTS_DIR /autofs/space/ocean_002/users/ANAT/SS_long' alias longsumalh 'suma -spec /autofs/space/ocean_002/users/ANAT/SS_long/avg_std_surf_C13/avg_std_lh.spec' alias longsumarh 'suma -spec /autofs/space/ocean_002/users/ANAT/SS_long/avg_std_surf_C13/avg_std_rh.spec' alias nssumalh 'suma -spec /autofs/space/ocean_002/users/ANAT/Northstar/Everest_pre/SUMA/stdmesh_sm/MapIco_lh_sm150_std.spec' alias nssumarh 'suma -spec /autofs/space/ocean_002/users/ANAT/Northstar/Everest_pre/SUMA/stdmesh_sm/MapIco_rh_sm150_std.spec' ## ## Prompt for tcsh set prompt = "%m:%n[\!] " umask 002 set filec set history=100 set savehist=80 set ignoreeof # Disable core dumps limit coredumpsize 0 if ($?prompt) then # I normally want my X stuff to display locally: setenv XENVIRONMENT ~/.Xenv