Help
This is a quick reference on programs I use.
DISCLAIMER:
This page is not
guaranteed to be up-to-date and is worth what you paid for
it. Internal programs may change at the will of the programmer.
Basic UNIX commands
Check out Mike's excellent internal
documentation
Don't forget to check out the
other helpful information found on his top page.
Jaz Info
sudo new_jaz 1
mount_jaz 1
mounts formatted jaz platter, cd
/jaz1/users
to use
unmount_jaz 1
unmounts jaz platter...ready to eject
~ona/bin/misc/checkjaz
hacky script that checks to see if any processes using jaz
platter, and if so prints them out (combination of fuser -c /jaz1 and ps -aux)
CD Info
Please make sure no other process, especially autobak, is running
before you attempt to write your data onto CD.
- Writing CDs
Mike's documentation on how to write to CDs on qtv-cd
~ona/bin/backup/autocdburn <dir>
Backs up contents of dir. dir must be absolute path name. Works only on qtv-cd
~ona/bin/backup/quikcdburn <dir>
~ona/bin/backup/dupcd
Duplicate CD in first tray onto CD in second tray. Repeating
cdburn will allow repeated burns on different CDs. Works only on
qtv-cd.
~ona/bin/misc/checkcd
hacky script that checks to see if any processes using your CD
Tape Info
Aliases
tapeget <dir>
gets dir directory/file off tape into current directory
tapeput <dir>
puts dir directory/file onto tape
Commands (for SunOS use /dev/rst0 instead)
mt -f /dev/rmt/0mn rewind
mt -f /dev/rmt/0mn rewoffl
rewinds tape and ejects it
mt -f /dev/rmt/0mn status
finds status of tapedrive
tar cvf /dev/rmt/0mn dir
stores file/directory dir onto tape
tar xvf /dev/rmt/0mn dir
retrieve file/directory from tape
tar tvf /dev/rmt/Omn
lists files stored on tape
~aschang/bin/tapedrives
checks status of tapedrives
~ona/bin/misc/duptape
backs up data from tape on cbv to mtt
Image Stuff
snapshot
can be used to take .ras images of xds files and then
converted to pict format
rasttopict
converts Sun ras images to more portable pict format
~ona/bin/rasttopictlist
same as above but can be used with list of files
SPM
~ona/bin/misc/motioncorrect
Motion corrects using Matlab 5.
Make sure you have the following in your .cshrc_Solaris_2:
setenv MATLABPATH ${MATLABPATH}:/space/gs/1/users/ona/spm96/sun
/space/gs/1/users/ona/spm96/sun
SPM96 on solaris, Matlab 5, SPM96 on SGI Matlab 4.2
/homes/nmrnew/home/thomas/spm95
SPM95 on sunos and SGI, Matlab 4.2
~ona/bin/convert/bsh2img
creates Analyze .img files along with headers assuming stack
of images
~ona/bin/spm/batch.m
example SPM96 batch file; can run with matlab as
matlab < batch.m >output.txt
Miscellaneous
~ona/bin/misc/airmotioncorrect
motion corrects using AIR3.08
- Elementary Functional MRI Data Analysis
/space/qtvraid/1/homes/ona/gcc/bin/gcc
gcc version 2.95.1 19990816 (release)
/opt/AcroRead/bin/acroread
/usr/local/bin/matlab5
/space/gs/32/users/splus6.0/bin/Splus
Last modified Sun Jan 17 21:41:18 EST 1999
Ona Wu
ona_at_nmr.mgh.harvard.edu
MGH-NMR Center
CNY-2301
13th Street, Bldg 149
Boston, MA 02129
(617) 643-3873 (o)
(617) 643-3939 (fax)